- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jmchilton: Merge next-stable.
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78597d2278e2/ Changeset: 78597d2278e2 User: jmchilton Date: 2014-12-17 14:41:26+00:00 Summary: Merge next-stable. Affected #: 3 files diff -r e614c7c1e0e9648076759c06dc33ed48b1847b13 -r 78597d2278e28ac962b80179d15eacd5849a4c79 test/functional/tools/gzipped_inputs.xml --- /dev/null +++ b/test/functional/tools/gzipped_inputs.xml @@ -0,0 +1,19 @@ +<tool id="gzipped_inputs" name="Echo Dataset"> + <command> + cat $input1 > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="4.bed.gz" /> + <output name="out_file1" file="4.bed" /> + </test> + </tests> + <help> + </help> +</tool> diff -r e614c7c1e0e9648076759c06dc33ed48b1847b13 -r 78597d2278e28ac962b80179d15eacd5849a4c79 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -13,6 +13,7 @@ <tool file="multi_output_assign_primary.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /> + <tool file="gzipped_inputs.xml" /><tool file="output_order.xml" /><tool file="output_format.xml" /><tool file="output_filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jmchilton: Fix gz/zip upload of files to test framework.
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a74d32014b05/ Changeset: a74d32014b05 Branch: next-stable User: jmchilton Date: 2014-12-17 14:38:49+00:00 Summary: Fix gz/zip upload of files to test framework. With test case to ensure they don't break again. Problem was due to a small switch of an if to an elif in 7114d15a6d22 which had been sort of masking over an older bug. Thanks to Peter Cock for reporting the issue. Affected #: 3 files diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -195,7 +195,9 @@ if isinstance( value, basic.DataToolParameter ): if not isinstance(param_value, list): param_value = [ param_value ] - processed_value = [ self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ) for v in param_value ] + map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ), +param_value ) + processed_value = param_value elif isinstance( value, basic.DataCollectionToolParameter ): assert 'collection' in param_extra collection_def = param_extra[ 'collection' ] diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd test/functional/tools/gzipped_inputs.xml --- /dev/null +++ b/test/functional/tools/gzipped_inputs.xml @@ -0,0 +1,19 @@ +<tool id="gzipped_inputs" name="Echo Dataset"> + <command> + cat $input1 > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="4.bed.gz" /> + <output name="out_file1" file="4.bed" /> + </test> + </tests> + <help> + </help> +</tool> diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -11,6 +11,7 @@ <tool file="multi_output_configured.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /> + <tool file="gzipped_inputs.xml" /><tool file="output_order.xml" /><tool file="output_format.xml" /><tool file="output_filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 5834b1066462
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7197e949d3ab/ Changeset: 7197e949d3ab Branch: stable User: natefoo Date: 2014-12-17 14:00:15+00:00 Summary: Update tag latest_2014.10.06 for changeset 5834b1066462 Affected #: 1 file diff -r 5834b1066462dd219f67c1c3cbd77c78e7cf3a6c -r 7197e949d3ab990ceb76c193ebc940d90aa04cad .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 +5834b1066462dd219f67c1c3cbd77c78e7cf3a6c latest_2014.10.06 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d13f2b265dbf/ Changeset: d13f2b265dbf User: Nitesh Turaga Date: 2014-12-16 16:04:58+00:00 Summary: "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also. Affected #: 1 file diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r d13f2b265dbf58c60ce4f13bcc902c4848c65c7c config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -136,7 +136,7 @@ # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). -#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml +#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool https://bitbucket.org/galaxy/galaxy-central/commits/e614c7c1e0e9/ Changeset: e614c7c1e0e9 User: dannon Date: 2014-12-16 20:48:44+00:00 Summary: Merged in nitesh1989/galaxy-central3 (pull request #615) "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also. Affected #: 1 file diff -r 1cf0af0a6324e24a0008f5ceff598573262f14ca -r e614c7c1e0e9648076759c06dc33ed48b1847b13 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -136,7 +136,7 @@ # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). -#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml +#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool 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.

1 0

commit/galaxy-central: dannon: Merged in nitesh1989/galaxy-central3 (pull request #615)
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e614c7c1e0e9/ Changeset: e614c7c1e0e9 User: dannon Date: 2014-12-16 20:48:44+00:00 Summary: Merged in nitesh1989/galaxy-central3 (pull request #615) "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also. Affected #: 1 file diff -r 1cf0af0a6324e24a0008f5ceff598573262f14ca -r e614c7c1e0e9648076759c06dc33ed48b1847b13 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -136,7 +136,7 @@ # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). -#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml +#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31f0b0cbb4ef/ Changeset: 31f0b0cbb4ef Branch: next-stable User: davebgx Date: 2014-12-16 20:15:57+00:00 Summary: Merge stable into next-stable. Affected #: 2 files diff -r d1f9d077c2288b25a35ae97e306cdf2924548d62 -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e416697be38e66f18be89a4cfca70457c9784294 latest_2014.10.06 +7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 diff -r d1f9d077c2288b25a35ae97e306cdf2924548d62 -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -322,8 +322,8 @@ return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name else: return "You already have a repository named <b>%s</b>, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." + if len( name ) < 2: + return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( name ) ): https://bitbucket.org/galaxy/galaxy-central/commits/1cf0af0a6324/ Changeset: 1cf0af0a6324 User: davebgx Date: 2014-12-16 20:16:18+00:00 Summary: Merge next-stable into default. Affected #: 2 files diff -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 -r 1cf0af0a6324e24a0008f5ceff598573262f14ca .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e416697be38e66f18be89a4cfca70457c9784294 latest_2014.10.06 +7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 diff -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 -r 1cf0af0a6324e24a0008f5ceff598573262f14ca lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -325,8 +325,8 @@ return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name else: return "You already have a repository named <b>%s</b>, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." + if len( name ) < 2: + return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( 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.

1 0

commit/galaxy-central: davebgx: Reduce minimum length of repository names from 4 characters to 2.
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5834b1066462/ Changeset: 5834b1066462 Branch: stable User: davebgx Date: 2014-12-16 20:00:50+00:00 Summary: Reduce minimum length of repository names from 4 characters to 2. Affected #: 1 file diff -r c265480083ecb81f1e968521932342137807601c -r 5834b1066462dd219f67c1c3cbd77c78e7cf3a6c lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -322,8 +322,8 @@ return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name else: return "You already have a repository named <b>%s</b>, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." + if len( name ) < 2: + return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( 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.

1 0

[galaxyproject/usegalaxy-playbook] d5c9a8: Updated shed tools on Test
by GitHub 16 Dec '14

16 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d5c9a8fcc4942c1e0b8d6a7edb118c243e6cc7cb https://github.com/galaxyproject/usegalaxy-playbook/commit/d5c9a8fcc4942c1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-16 (Tue, 16 Dec 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Updated shed tools on Test Commit: 8977b7af2dd8512a34aaa3dcbd7711a54d6c1228 https://github.com/galaxyproject/usegalaxy-playbook/commit/8977b7af2dd8512a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-16 (Tue, 16 Dec 2014) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Remove downtime banner. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e8119d8b39f7...…

1 0

commit/galaxy-central: guerler: ToolForm: Minor UI adjustments
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1210ec537026/ Changeset: 1210ec537026 User: guerler Date: 2014-12-16 18:24:42+00:00 Summary: ToolForm: Minor UI adjustments Affected #: 6 files diff -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -321,23 +321,6 @@ // create message view this.message = new Ui.Message(); - // construct tool requirements message content - var requirements_message = 'This tool requires '; - for (var i in options.requirements) { - var req = options.requirements[i]; - requirements_message += req.name; - if (req.version) { - requirements_message += ' (Version ' + req.version + ')'; - } - if (i < options.requirements.length - 2) { - requirements_message += ', '; - } - if (i == options.requirements.length - 2) { - requirements_message += ' and '; - } - } - requirements_message += '.'; - // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', @@ -348,8 +331,8 @@ this.visible = true; self.message.update({ persistent : true, - message : requirements_message, - status : 'warning' + message : ToolTemplate.requirements(options), + status : 'info' }); } else { this.visible = false; @@ -395,7 +378,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ - icon : 'fa-gear', + icon : 'fa-caret-down', title : 'Options', tooltip : 'View available options' }); @@ -462,7 +445,7 @@ // create portlet this.portlet = new Portlet.View({ icon : 'fa-wrench', - title : '<b>' + options.name + '</b> ' + options.description + ' (Version ' + options.version + ')', + title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Tool Version ' + options.version + ')', cls : 'ui-portlet-slim', operations: { requirements : requirements_button, diff -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -58,6 +58,24 @@ '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; + }, + + requirements: function(options) { + var requirements_message = 'This tool requires '; + for (var i in options.requirements) { + var req = options.requirements[i]; + requirements_message += req.name; + if (req.version) { + requirements_message += ' (Version ' + req.version + ')'; + } + if (i < options.requirements.length - 2) { + requirements_message += ', '; + } + if (i == options.requirements.length - 2) { + requirements_message += ' and '; + } + } + return requirements_message + '. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'; } }; diff -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -321,23 +321,6 @@ // create message view this.message = new Ui.Message(); - // construct tool requirements message content - var requirements_message = 'This tool requires '; - for (var i in options.requirements) { - var req = options.requirements[i]; - requirements_message += req.name; - if (req.version) { - requirements_message += ' (Version ' + req.version + ')'; - } - if (i < options.requirements.length - 2) { - requirements_message += ', '; - } - if (i == options.requirements.length - 2) { - requirements_message += ' and '; - } - } - requirements_message += '.'; - // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', @@ -348,8 +331,8 @@ this.visible = true; self.message.update({ persistent : true, - message : requirements_message, - status : 'warning' + message : ToolTemplate.requirements(options), + status : 'info' }); } else { this.visible = false; @@ -395,7 +378,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ - icon : 'fa-gear', + icon : 'fa-caret-down', title : 'Options', tooltip : 'View available options' }); @@ -462,7 +445,7 @@ // create portlet this.portlet = new Portlet.View({ icon : 'fa-wrench', - title : '<b>' + options.name + '</b> ' + options.description + ' (Version ' + options.version + ')', + title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Tool Version ' + options.version + ')', cls : 'ui-portlet-slim', operations: { requirements : requirements_button, diff -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -58,6 +58,24 @@ '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; + }, + + requirements: function(options) { + var requirements_message = 'This tool requires '; + for (var i in options.requirements) { + var req = options.requirements[i]; + requirements_message += req.name; + if (req.version) { + requirements_message += ' (Version ' + req.version + ')'; + } + if (i < options.requirements.length - 2) { + requirements_message += ', '; + } + if (i == options.requirements.length - 2) { + requirements_message += ' and '; + } + } + return requirements_message + '. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'; } }; diff -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var o=parent.Galaxy;if(o&&o.modal){this.modal=o.modal}else{this.modal=new m.Modal.View()}if(o&&o.currUser){this.is_admin=o.currUser.get("is_admin")}else{this.is_admin=false}this.options=n;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(n){$(this.container).empty();$(this.container).append(n)},highlight:function(o,p,n){var q=this.element_list[o];if(q){q.error(p||"Please verify this parameter.");if(!n){$(this.container).animate({scrollTop:q.$el.offset().top-20},500)}}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{o+="tool_version="+this.options.version+"&";var q=top.location.href;var r=q.indexOf("?");if(q.indexOf("tool_id=")!=-1&&r!==-1){o+=q.slice(r+1)}}}var p=this.deferred.register();i.request({type:"GET",url:o,success:function(s){n.options=s;n._buildForm();n.message.update({status:"success",message:"Now you are using '"+n.options.name+"' version "+n.options.version+".",persistent:false});n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(s)},error:function(s){n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(s);var t=s.error||"Uncaught error.";n.modal.show({title:"Tool cannot be executed",body:t,buttons:{Close:function(){n.modal.hide()}}})}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(s){if(s.values.length>0&&s.values[0]&&s.values[0].src==="hda"){return n.content.get({id:s.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function r(v){for(var t in n.input_list){var u=n.field_list[t];var s=n.input_list[t];if(s.is_dynamic&&u.wait&&u.unwait){if(v){u.wait()}else{u.unwait()}}}}r(true);var q=this.deferred.register();var p=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;i.request({type:"GET",url:p,data:o,success:function(s){n.tree.matchModel(s,function(u,y){var t=n.input_list[u];if(t&&t.options){if(!_.isEqual(t.options,y.options)){t.options=y.options;var z=n.field_list[u];if(z.update){var x=[];if((["data","data_collection","drill_down"]).indexOf(t.type)!=-1){x=t.options}else{for(var w in y.options){var v=y.options[w];if(v.length>2){x.push({label:v[0],value:v[1]})}}}z.update(x);z.trigger("change");console.debug("Updating options for "+u)}}}});r(false);n.deferred.done(q);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(s)},error:function(s){n.deferred.done(q);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(s)}})},_buildForm:function(){var n=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);var p=this.options;this._renderForm(p);this.tree.finalize();if(p.errors){var q=this.tree.matchResponse(p.errors);for(var o in q){this.highlight(o,q[o],true)}}this.on("refresh",function(){n.deferred.reset();n.deferred.execute(function(){n._updateModel()})});this.on("reset",function(){for(var r in this.element_list){this.element_list[r].reset()}})},_renderForm:function(y){var x=this;this.message=new m.Message();var n="This tool requires ";for(var r in y.requirements){var w=y.requirements[r];n+=w.name;if(w.version){n+=" (Version "+w.version+")"}if(r<y.requirements.length-2){n+=", "}if(r==y.requirements.length-2){n+=" and "}}n+=".";var t=new m.ButtonIcon({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;x.message.update({persistent:true,message:n,status:"warning"})}else{this.visible=false;x.message.update({message:""})}}});if(!y.requirements||y.requirements.length==0){t.$el.hide()}var p=new m.ButtonMenu({icon:"fa-cubes",title:"Versions",tooltip:"Select another tool version"});if(y.versions&&y.versions.length>1){for(var r in y.versions){var u=y.versions[r];if(u!=y.version){p.addMenu({title:"Switch to "+u,version:u,icon:"fa-cube",onclick:function(){y.id=y.id.replace(y.version,this.version);y.version=this.version;x.deferred.reset();x.deferred.execute(function(){x._buildModel()})}})}}}else{p.$el.hide()}var s=new m.ButtonMenu({icon:"fa-gear",title:"Options",tooltip:"View available options"});if(y.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(y.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(y.biostar_url+"/t/"+y.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+y.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+y.id+"/download"}})}this.section=new l.View(x,{inputs:y.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+y.name+"</b> "+y.description+" (Version "+y.version+")",cls:"ui-portlet-slim",operations:{requirements:t,menu:s,versions:p},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute: "+y.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){x.job_handler.submit()}})}});this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(y.help!=""){this.$el.append(d.help(y.help))}if(y.citations){var v=$("<div/>");var o=new k.ToolCitationCollection();o.tool_id=y.id;var q=new a.CitationListView({el:v,collection:o});q.render();o.fetch();this.$el.append(v)}if(y.message){this.message.update({persistent:true,status:"warning",message:y.message})}}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var o=parent.Galaxy;if(o&&o.modal){this.modal=o.modal}else{this.modal=new m.Modal.View()}if(o&&o.currUser){this.is_admin=o.currUser.get("is_admin")}else{this.is_admin=false}this.options=n;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(n){$(this.container).empty();$(this.container).append(n)},highlight:function(o,p,n){var q=this.element_list[o];if(q){q.error(p||"Please verify this parameter.");if(!n){$(this.container).animate({scrollTop:q.$el.offset().top-20},500)}}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{o+="tool_version="+this.options.version+"&";var q=top.location.href;var r=q.indexOf("?");if(q.indexOf("tool_id=")!=-1&&r!==-1){o+=q.slice(r+1)}}}var p=this.deferred.register();i.request({type:"GET",url:o,success:function(s){n.options=s;n._buildForm();n.message.update({status:"success",message:"Now you are using '"+n.options.name+"' version "+n.options.version+".",persistent:false});n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(s)},error:function(s){n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(s);var t=s.error||"Uncaught error.";n.modal.show({title:"Tool cannot be executed",body:t,buttons:{Close:function(){n.modal.hide()}}})}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(s){if(s.values.length>0&&s.values[0]&&s.values[0].src==="hda"){return n.content.get({id:s.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function r(v){for(var t in n.input_list){var u=n.field_list[t];var s=n.input_list[t];if(s.is_dynamic&&u.wait&&u.unwait){if(v){u.wait()}else{u.unwait()}}}}r(true);var q=this.deferred.register();var p=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;i.request({type:"GET",url:p,data:o,success:function(s){n.tree.matchModel(s,function(u,y){var t=n.input_list[u];if(t&&t.options){if(!_.isEqual(t.options,y.options)){t.options=y.options;var z=n.field_list[u];if(z.update){var x=[];if((["data","data_collection","drill_down"]).indexOf(t.type)!=-1){x=t.options}else{for(var w in y.options){var v=y.options[w];if(v.length>2){x.push({label:v[0],value:v[1]})}}}z.update(x);z.trigger("change");console.debug("Updating options for "+u)}}}});r(false);n.deferred.done(q);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(s)},error:function(s){n.deferred.done(q);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(s)}})},_buildForm:function(){var n=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);var p=this.options;this._renderForm(p);this.tree.finalize();if(p.errors){var q=this.tree.matchResponse(p.errors);for(var o in q){this.highlight(o,q[o],true)}}this.on("refresh",function(){n.deferred.reset();n.deferred.execute(function(){n._updateModel()})});this.on("reset",function(){for(var r in this.element_list){this.element_list[r].reset()}})},_renderForm:function(w){var v=this;this.message=new m.Message();var s=new m.ButtonIcon({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;v.message.update({persistent:true,message:d.requirements(w),status:"info"})}else{this.visible=false;v.message.update({message:""})}}});if(!w.requirements||w.requirements.length==0){s.$el.hide()}var o=new m.ButtonMenu({icon:"fa-cubes",title:"Versions",tooltip:"Select another tool version"});if(w.versions&&w.versions.length>1){for(var q in w.versions){var t=w.versions[q];if(t!=w.version){o.addMenu({title:"Switch to "+t,version:t,icon:"fa-cube",onclick:function(){w.id=w.id.replace(w.version,this.version);w.version=this.version;v.deferred.reset();v.deferred.execute(function(){v._buildModel()})}})}}}else{o.$el.hide()}var r=new m.ButtonMenu({icon:"fa-caret-down",title:"Options",tooltip:"View available options"});if(w.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(w.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(w.biostar_url+"/t/"+w.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+w.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+w.id+"/download"}})}this.section=new l.View(v,{inputs:w.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+w.name+"</b> "+w.description+" (Galaxy Tool Version "+w.version+")",cls:"ui-portlet-slim",operations:{requirements:s,menu:r,versions:o},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute: "+w.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){v.job_handler.submit()}})}});this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(w.help!=""){this.$el.append(d.help(w.help))}if(w.citations){var u=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=w.id;var p=new a.CitationListView({el:u,collection:n});p.render();n.fetch();this.$el.append(u)}if(w.message){this.message.update({persistent:true,status:"warning",message:w.message})}}});return{View:b}}); \ No newline at end of file diff -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Improve form update and job submission
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/17933aef1d35/ Changeset: 17933aef1d35 User: guerler Date: 2014-12-16 16:45:40+00:00 Summary: ToolForm: Improve form update and job submission Affected #: 15 files diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -17,9 +17,6 @@ // log options console.debug(options); - // link this - var self = this; - // link galaxy modal or create one var galaxy = parent.Galaxy; if (galaxy && galaxy.modal) { @@ -52,38 +49,35 @@ this._buildForm(); }, - // reciept shows the final message usually upon successful job submission + /** Shows the final message (usually upon successful job submission) + */ reciept: function($el) { $(this.container).empty(); $(this.container).append($el); }, - - // reset form - reset: function() { - for (var i in this.element_list) { - this.element_list[i].reset(); + + /** Highlight and scroll to input element (currently only used for error notifications) + */ + highlight: function (input_id, message, silent) { + // get input field + var input_element = this.element_list[input_id]; + + // check input element + if (input_element) { + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // scroll to first input element + if (!silent) { + $(this.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + } } }, - // rebuild underlying data structure representation for the tool form - // this happens i.e. when repeat blocks are added or removed and on initialization - rebuild: function() { - this.tree.refresh(); - console.debug('tools-form::rebuild() - Rebuilding data structures.'); - }, - - // refreshes input states i.e. for dynamic parameters - refresh: function() { - // only refresh the state if the form contains dynamic parameters - // by using/reseting the deferred ajax queue the number of redundant calls is reduced - if (this.is_dynamic) { - var self = this; - this.deferred.reset(); - this.deferred.execute(function(){self._updateModel()}); - }; - }, - - // build tool model through api call + /** Builds a new model through api call and recreates the entire form + */ _buildModel: function() { // link this var self = this; @@ -156,7 +150,8 @@ }); }, - // request a new model and update the form inputs + /** Request a new model for an already created tool form and updates the form inputs + */ _updateModel: function() { // create the request dictionary var self = this; @@ -202,9 +197,39 @@ type : 'GET', url : model_url, data : current_state, - success : function(response) { - // rebuild form - self._updateForm(response); + success : function(new_model) { + // update form + self.tree.matchModel(new_model, function(input_id, node) { + var input = self.input_list[input_id]; + if (input && input.options) { + if (!_.isEqual(input.options, node.options)) { + // backup new options + input.options = node.options; + + // get/update field + var field = self.field_list[input_id]; + if (field.update) { + var new_options = []; + if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) { + new_options = input.options; + } else { + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } + } + field.update(new_options); + field.trigger('change'); + console.debug('Updating options for ' + input_id); + } + } + } + }); // unset wait mode wait(false); @@ -214,7 +239,7 @@ // log success console.debug('tools-form::_refreshForm() - States refreshed.'); - console.debug(response); + console.debug(new_model); }, error : function(response) { // process completed @@ -227,47 +252,16 @@ }); }, - // update form inputs - _updateForm: function(new_model) { - var self = this; - this.tree.matchModel(new_model, function(input_id, node) { - var input = self.input_list[input_id]; - if (input && input.options) { - if (!_.isEqual(input.options, node.options)) { - // backup new options - input.options = node.options; - - // get/update field - var field = self.field_list[input_id]; - if (field.update) { - var new_options = []; - if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) { - new_options = input.options; - } else { - for (var i in node.options) { - var opt = node.options[i]; - if (opt.length > 2) { - new_options.push({ - 'label': opt[0], - 'value': opt[1] - }); - } - } - } - field.update(new_options); - field.trigger('change'); - console.debug('Updating options for ' + input_id); - } - } - } - }); - }, - - // builds the tool form + /** Main tool form build function. This function is called once a new model is available. + */ _buildForm: function() { // link this var self = this; + // reset events + this.off('refresh'); + this.off('reset'); + // reset field list, which contains the input field elements this.field_list = {}; @@ -289,6 +283,41 @@ // link model options var options = this.options; + // create ui elements + this._renderForm(options); + + // rebuild the underlying data structure + this.tree.finalize(); + + // show errors + if (options.errors) { + var error_messages = this.tree.matchResponse(options.errors); + for (var input_id in error_messages) { + this.highlight(input_id, error_messages[input_id], true); + } + } + + // add refresh listener + this.on('refresh', function() { + // by using/reseting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel()}); + }); + + // add reset listener + this.on('reset', function() { + for (var i in this.element_list) { + this.element_list[i].reset(); + } + }); + }, + + /** Renders the UI elements required for the form + */ + _renderForm: function(options) { + // link this + var self = this; + // create message view this.message = new Ui.Message(); @@ -454,6 +483,12 @@ } }); + // append message + this.portlet.append(this.message.$el, true); + + // append tool section + this.portlet.append(this.section.$el); + // start form this.$el.empty(); this.$el.append(this.portlet.$el); @@ -474,15 +509,6 @@ this.$el.append($citations); } - // append message - this.portlet.append(this.message.$el, true); - - // append tool section - this.portlet.append(this.section.$el); - - // rebuild the underlying data structure - this.rebuild(); - // show message if available in model if (options.message) { this.message.update({ @@ -491,38 +517,6 @@ message : options.message }); } - - // show errors - this._showErrors(options); - }, - - /** Highlight all errors - */ - _showErrors: function(options) { - if (options.errors) { - this.tree.finalize(); - var error_messages = this.tree.matchResponse(options.errors); - for (var input_id in error_messages) { - this.foundError(input_id, error_messages[input_id], true); - } - } - }, - - /** Highlight and scroll to error - */ - foundError: function (input_id, message, silent) { - // get input field - var input_element = this.element_list[input_id]; - - // mark error - input_element.error(message || 'Please verify this parameter.'); - - // scroll to first input element - if (!silent) { - $(this.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - } } }); diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -63,7 +63,7 @@ if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); - this.app.refresh(); + this.app.trigger('refresh'); } else { this.$field.hide(); this.$title_optional.html('Enable'); diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac 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 @@ -22,7 +22,7 @@ } // reset - this.app.reset(); + this.app.trigger('reset'); // validate job definition if (!this._validation(job_def)) { @@ -51,7 +51,7 @@ if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { - self.app.foundError(input_id, error_messages[input_id]); + self.app.highlight(input_id, error_messages[input_id]); break; } } else { @@ -99,7 +99,7 @@ // validate non-optional fields if (!input_def.optional && input_field.validate && !input_field.validate()) { - this.app.foundError(input_id); + this.app.highlight(input_id); return false; } @@ -120,7 +120,7 @@ batch_src = src; } else { if (batch_src !== src) { - this.app.foundError(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.'); + this.app.highlight(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.'); return false; } } @@ -131,7 +131,7 @@ batch_n = n; } else { if (batch_n !== n) { - this.app.foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + this.app.highlight(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -119,7 +119,7 @@ } // refresh form inputs - self.app.refresh(); + self.app.trigger('refresh'); }; // add conditional sub sections @@ -172,8 +172,7 @@ repeat.retitle(input_def.title); // trigger refresh - self.app.rebuild(); - self.app.refresh(); + self.app.trigger('refresh'); } } @@ -206,8 +205,7 @@ create(input_def.inputs, true); // trigger refresh - self.app.rebuild(); - self.app.refresh(); + self.app.trigger('refresh'); } }); @@ -255,11 +253,6 @@ // create input field var field = this._createField(input_def); - // flagging this form as dynamic will trigger api-driven refresh events - if (input_def.is_dynamic) { - this.app.is_dynamic = true; - } - // add to field list this.app.field_list[id] = field; @@ -392,7 +385,7 @@ type : input_def.type, data : input_def.options, onchange : function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, @@ -430,7 +423,7 @@ multiple : input_def.multiple, searchable : input_def.searchable, onchange : function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, @@ -444,7 +437,7 @@ data : input_def.options, display : input_def.display, onchange : function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, @@ -457,7 +450,7 @@ id : 'field-' + input_def.id, area : input_def.area, onchange: function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -1,5 +1,5 @@ /* - This class maps the tool form to javascript datastructures. Once refreshed it converts the tool form (including sub sections) into a xml (containing only ids) and a detailed dictionary representation. The xml object is a jquery element and can be searched/filtered e.g. in order to hierarchically identify referenced fields. Once the job is ready for submission, the finalize function will transform the generic dictionary representation into the specific flat dictionary format required by the tools api. + This class maps the tool form dom to an api compatible javascript dictionary. */ // dependencies define([], function() { @@ -11,43 +11,39 @@ this.app = app; }, - /** Refresh the datastructures representing the ToolForm. + /** Convert dictionary representation into tool api specific flat dictionary format. */ - refresh: function() { - // create dictionary - this.dict = {}; + finalize: function(patch) { + // link this + var self = this; - // create xml object - this.xml = $('<div/>'); - + // dictionary with api specific identifiers + this.map_dict = {}; + // check if section is available if (!this.app.section) { return {}; } - // fill dictionary - this._iterate(this.app.section.$el, this.dict, this.xml); - }, - - /** Convert dictionary representation into tool api specific flat dictionary format. - */ - finalize: function(patch) { - // initialize + // ensure that dictionary with patching functions exists patch = patch || {}; - // link this - var self = this; + // dictionary formatted for job submission or tool form update + var result_dict = {}; + + // prepare full dictionary + var dict = {}; - // dictionary formatted for job submission - this.job_def = {}; - - // dictionary with api specific identifiers - this.job_ids = {}; - + // fill dictionary from dom + this._iterate(this.app.section.$el, dict); + // add identifier and value to job definition function add(job_input_id, input_id, input_value) { - self.job_def[job_input_id] = input_value; - self.job_ids[job_input_id] = input_id; + // add entry to result dictionary + result_dict[job_input_id] = input_value; + + // backup id mapping + self.map_dict[job_input_id] = input_id; }; // converter between raw dictionary and job dictionary @@ -135,16 +131,16 @@ } // start conversion - convert('', this.dict); + convert('', dict); // return result - return this.job_def; + return result_dict; }, /** Match job definition identifier to input element identifier */ match: function (job_input_id) { - return this.job_ids && this.job_ids[job_input_id]; + return this.map_dict && this.map_dict[job_input_id]; }, /** Match conditional values to selected cases @@ -201,7 +197,7 @@ } break; default: - var input_id = self.job_ids[index]; + var input_id = self.map_dict[index]; if (input_id) { callback(input_id, node); } @@ -228,7 +224,7 @@ // search throughout response function search (id, head) { if (typeof head === 'string') { - var input_id = self.job_ids[id]; + var input_id = self.map_dict[id]; if (input_id) { result[input_id] = head; } @@ -254,83 +250,9 @@ return result; }, - /** Find referenced elements. + /** Iterate through the tool form dom and map it to the dictionary. */ - references: function(identifier, type) { - // referenced elements - var referenced = []; - - // link this - var self = this; - - // iterate - function search (name, parent) { - // get child nodes - var children = $(parent).children(); - - // create list of referenced elements - var list = []; - - // a node level is skipped if a reference of higher priority was found - var skip = false; - - // verify that hierarchy level is referenced by target identifier - children.each(function() { - // get child element - var child = this; - - // get id - var id = $(child).attr('id'); - - // skip target element - if (id !== identifier) { - // get input element - var input = self.app.input_list[id]; - if (input) { - // check for new reference definition with higher priority - if (input.name == name) { - // skip iteration for this branch - skip = true; - return false; - } - - // check for referenced element - if (input.data_ref == name && input.type == type) { - list.push(id); - } - } - } - }); - - // skip iteration - if (!skip) { - // merge temporary list with result - referenced = referenced.concat(list); - - // continue iteration - children.each(function() { - search(name, this); - }); - } - } - - // get initial node - var node = this.xml.find('#' + identifier); - if (node.length > 0) { - // get parent input element - var input = this.app.input_list[identifier]; - if (input) { - search(input.name, node.parent()); - } - } - - // return - return referenced; - }, - - /** Iterate through the tool form dom and map it to the dictionary and xml representation. - */ - _iterate: function(parent, dict, xml) { + _iterate: function(parent, dict) { // get child nodes var self = this; var children = $(parent).children(); @@ -354,16 +276,10 @@ } } - // create xml element - var $el = $('<div id="' + id + '"/>'); - - // append xml - xml.append($el); - // fill sub dictionary - self._iterate(child, dict[id], $el); + self._iterate(child, dict[id]); } else { - self._iterate(child, dict, xml); + self._iterate(child, dict); } }); } diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -17,9 +17,6 @@ // log options console.debug(options); - // link this - var self = this; - // link galaxy modal or create one var galaxy = parent.Galaxy; if (galaxy && galaxy.modal) { @@ -52,38 +49,35 @@ this._buildForm(); }, - // reciept shows the final message usually upon successful job submission + /** Shows the final message (usually upon successful job submission) + */ reciept: function($el) { $(this.container).empty(); $(this.container).append($el); }, - - // reset form - reset: function() { - for (var i in this.element_list) { - this.element_list[i].reset(); + + /** Highlight and scroll to input element (currently only used for error notifications) + */ + highlight: function (input_id, message, silent) { + // get input field + var input_element = this.element_list[input_id]; + + // check input element + if (input_element) { + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // scroll to first input element + if (!silent) { + $(this.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + } } }, - // rebuild underlying data structure representation for the tool form - // this happens i.e. when repeat blocks are added or removed and on initialization - rebuild: function() { - this.tree.refresh(); - console.debug('tools-form::rebuild() - Rebuilding data structures.'); - }, - - // refreshes input states i.e. for dynamic parameters - refresh: function() { - // only refresh the state if the form contains dynamic parameters - // by using/reseting the deferred ajax queue the number of redundant calls is reduced - if (this.is_dynamic) { - var self = this; - this.deferred.reset(); - this.deferred.execute(function(){self._updateModel()}); - }; - }, - - // build tool model through api call + /** Builds a new model through api call and recreates the entire form + */ _buildModel: function() { // link this var self = this; @@ -156,7 +150,8 @@ }); }, - // request a new model and update the form inputs + /** Request a new model for an already created tool form and updates the form inputs + */ _updateModel: function() { // create the request dictionary var self = this; @@ -202,9 +197,39 @@ type : 'GET', url : model_url, data : current_state, - success : function(response) { - // rebuild form - self._updateForm(response); + success : function(new_model) { + // update form + self.tree.matchModel(new_model, function(input_id, node) { + var input = self.input_list[input_id]; + if (input && input.options) { + if (!_.isEqual(input.options, node.options)) { + // backup new options + input.options = node.options; + + // get/update field + var field = self.field_list[input_id]; + if (field.update) { + var new_options = []; + if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) { + new_options = input.options; + } else { + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } + } + field.update(new_options); + field.trigger('change'); + console.debug('Updating options for ' + input_id); + } + } + } + }); // unset wait mode wait(false); @@ -214,7 +239,7 @@ // log success console.debug('tools-form::_refreshForm() - States refreshed.'); - console.debug(response); + console.debug(new_model); }, error : function(response) { // process completed @@ -227,47 +252,16 @@ }); }, - // update form inputs - _updateForm: function(new_model) { - var self = this; - this.tree.matchModel(new_model, function(input_id, node) { - var input = self.input_list[input_id]; - if (input && input.options) { - if (!_.isEqual(input.options, node.options)) { - // backup new options - input.options = node.options; - - // get/update field - var field = self.field_list[input_id]; - if (field.update) { - var new_options = []; - if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) { - new_options = input.options; - } else { - for (var i in node.options) { - var opt = node.options[i]; - if (opt.length > 2) { - new_options.push({ - 'label': opt[0], - 'value': opt[1] - }); - } - } - } - field.update(new_options); - field.trigger('change'); - console.debug('Updating options for ' + input_id); - } - } - } - }); - }, - - // builds the tool form + /** Main tool form build function. This function is called once a new model is available. + */ _buildForm: function() { // link this var self = this; + // reset events + this.off('refresh'); + this.off('reset'); + // reset field list, which contains the input field elements this.field_list = {}; @@ -289,6 +283,41 @@ // link model options var options = this.options; + // create ui elements + this._renderForm(options); + + // rebuild the underlying data structure + this.tree.finalize(); + + // show errors + if (options.errors) { + var error_messages = this.tree.matchResponse(options.errors); + for (var input_id in error_messages) { + this.highlight(input_id, error_messages[input_id], true); + } + } + + // add refresh listener + this.on('refresh', function() { + // by using/reseting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel()}); + }); + + // add reset listener + this.on('reset', function() { + for (var i in this.element_list) { + this.element_list[i].reset(); + } + }); + }, + + /** Renders the UI elements required for the form + */ + _renderForm: function(options) { + // link this + var self = this; + // create message view this.message = new Ui.Message(); @@ -454,6 +483,12 @@ } }); + // append message + this.portlet.append(this.message.$el, true); + + // append tool section + this.portlet.append(this.section.$el); + // start form this.$el.empty(); this.$el.append(this.portlet.$el); @@ -474,15 +509,6 @@ this.$el.append($citations); } - // append message - this.portlet.append(this.message.$el, true); - - // append tool section - this.portlet.append(this.section.$el); - - // rebuild the underlying data structure - this.rebuild(); - // show message if available in model if (options.message) { this.message.update({ @@ -491,38 +517,6 @@ message : options.message }); } - - // show errors - this._showErrors(options); - }, - - /** Highlight all errors - */ - _showErrors: function(options) { - if (options.errors) { - this.tree.finalize(); - var error_messages = this.tree.matchResponse(options.errors); - for (var input_id in error_messages) { - this.foundError(input_id, error_messages[input_id], true); - } - } - }, - - /** Highlight and scroll to error - */ - foundError: function (input_id, message, silent) { - // get input field - var input_element = this.element_list[input_id]; - - // mark error - input_element.error(message || 'Please verify this parameter.'); - - // scroll to first input element - if (!silent) { - $(this.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - } } }); diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -63,7 +63,7 @@ if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); - this.app.refresh(); + this.app.trigger('refresh'); } else { this.$field.hide(); this.$title_optional.html('Enable'); diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -22,7 +22,7 @@ } // reset - this.app.reset(); + this.app.trigger('reset'); // validate job definition if (!this._validation(job_def)) { @@ -51,7 +51,7 @@ if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { - self.app.foundError(input_id, error_messages[input_id]); + self.app.highlight(input_id, error_messages[input_id]); break; } } else { @@ -99,7 +99,7 @@ // validate non-optional fields if (!input_def.optional && input_field.validate && !input_field.validate()) { - this.app.foundError(input_id); + this.app.highlight(input_id); return false; } @@ -120,7 +120,7 @@ batch_src = src; } else { if (batch_src !== src) { - this.app.foundError(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.'); + this.app.highlight(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.'); return false; } } @@ -131,7 +131,7 @@ batch_n = n; } else { if (batch_n !== n) { - this.app.foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + this.app.highlight(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -119,7 +119,7 @@ } // refresh form inputs - self.app.refresh(); + self.app.trigger('refresh'); }; // add conditional sub sections @@ -172,8 +172,7 @@ repeat.retitle(input_def.title); // trigger refresh - self.app.rebuild(); - self.app.refresh(); + self.app.trigger('refresh'); } } @@ -206,8 +205,7 @@ create(input_def.inputs, true); // trigger refresh - self.app.rebuild(); - self.app.refresh(); + self.app.trigger('refresh'); } }); @@ -255,11 +253,6 @@ // create input field var field = this._createField(input_def); - // flagging this form as dynamic will trigger api-driven refresh events - if (input_def.is_dynamic) { - this.app.is_dynamic = true; - } - // add to field list this.app.field_list[id] = field; @@ -392,7 +385,7 @@ type : input_def.type, data : input_def.options, onchange : function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, @@ -430,7 +423,7 @@ multiple : input_def.multiple, searchable : input_def.searchable, onchange : function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, @@ -444,7 +437,7 @@ data : input_def.options, display : input_def.display, onchange : function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, @@ -457,7 +450,7 @@ id : 'field-' + input_def.id, area : input_def.area, onchange: function() { - self.app.refresh(); + self.app.trigger('refresh'); } }); }, diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -1,5 +1,5 @@ /* - This class maps the tool form to javascript datastructures. Once refreshed it converts the tool form (including sub sections) into a xml (containing only ids) and a detailed dictionary representation. The xml object is a jquery element and can be searched/filtered e.g. in order to hierarchically identify referenced fields. Once the job is ready for submission, the finalize function will transform the generic dictionary representation into the specific flat dictionary format required by the tools api. + This class maps the tool form dom to an api compatible javascript dictionary. */ // dependencies define([], function() { @@ -11,43 +11,39 @@ this.app = app; }, - /** Refresh the datastructures representing the ToolForm. + /** Convert dictionary representation into tool api specific flat dictionary format. */ - refresh: function() { - // create dictionary - this.dict = {}; + finalize: function(patch) { + // link this + var self = this; - // create xml object - this.xml = $('<div/>'); - + // dictionary with api specific identifiers + this.map_dict = {}; + // check if section is available if (!this.app.section) { return {}; } - // fill dictionary - this._iterate(this.app.section.$el, this.dict, this.xml); - }, - - /** Convert dictionary representation into tool api specific flat dictionary format. - */ - finalize: function(patch) { - // initialize + // ensure that dictionary with patching functions exists patch = patch || {}; - // link this - var self = this; + // dictionary formatted for job submission or tool form update + var result_dict = {}; + + // prepare full dictionary + var dict = {}; - // dictionary formatted for job submission - this.job_def = {}; - - // dictionary with api specific identifiers - this.job_ids = {}; - + // fill dictionary from dom + this._iterate(this.app.section.$el, dict); + // add identifier and value to job definition function add(job_input_id, input_id, input_value) { - self.job_def[job_input_id] = input_value; - self.job_ids[job_input_id] = input_id; + // add entry to result dictionary + result_dict[job_input_id] = input_value; + + // backup id mapping + self.map_dict[job_input_id] = input_id; }; // converter between raw dictionary and job dictionary @@ -135,16 +131,16 @@ } // start conversion - convert('', this.dict); + convert('', dict); // return result - return this.job_def; + return result_dict; }, /** Match job definition identifier to input element identifier */ match: function (job_input_id) { - return this.job_ids && this.job_ids[job_input_id]; + return this.map_dict && this.map_dict[job_input_id]; }, /** Match conditional values to selected cases @@ -201,7 +197,7 @@ } break; default: - var input_id = self.job_ids[index]; + var input_id = self.map_dict[index]; if (input_id) { callback(input_id, node); } @@ -228,7 +224,7 @@ // search throughout response function search (id, head) { if (typeof head === 'string') { - var input_id = self.job_ids[id]; + var input_id = self.map_dict[id]; if (input_id) { result[input_id] = head; } @@ -254,83 +250,9 @@ return result; }, - /** Find referenced elements. + /** Iterate through the tool form dom and map it to the dictionary. */ - references: function(identifier, type) { - // referenced elements - var referenced = []; - - // link this - var self = this; - - // iterate - function search (name, parent) { - // get child nodes - var children = $(parent).children(); - - // create list of referenced elements - var list = []; - - // a node level is skipped if a reference of higher priority was found - var skip = false; - - // verify that hierarchy level is referenced by target identifier - children.each(function() { - // get child element - var child = this; - - // get id - var id = $(child).attr('id'); - - // skip target element - if (id !== identifier) { - // get input element - var input = self.app.input_list[id]; - if (input) { - // check for new reference definition with higher priority - if (input.name == name) { - // skip iteration for this branch - skip = true; - return false; - } - - // check for referenced element - if (input.data_ref == name && input.type == type) { - list.push(id); - } - } - } - }); - - // skip iteration - if (!skip) { - // merge temporary list with result - referenced = referenced.concat(list); - - // continue iteration - children.each(function() { - search(name, this); - }); - } - } - - // get initial node - var node = this.xml.find('#' + identifier); - if (node.length > 0) { - // get parent input element - var input = this.app.input_list[identifier]; - if (input) { - search(input.name, node.parent()); - } - } - - // return - return referenced; - }, - - /** Iterate through the tool form dom and map it to the dictionary and xml representation. - */ - _iterate: function(parent, dict, xml) { + _iterate: function(parent, dict) { // get child nodes var self = this; var children = $(parent).children(); @@ -354,16 +276,10 @@ } } - // create xml element - var $el = $('<div id="' + id + '"/>'); - - // append xml - xml.append($el); - // fill sub dictionary - self._iterate(child, dict[id], $el); + self._iterate(child, dict[id]); } else { - self._iterate(child, dict, xml); + self._iterate(child, dict); } }); } diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{o+="tool_version="+this.options.version+"&";var q=top.location.href;var r=q.indexOf("?");if(q.indexOf("tool_id=")!=-1&&r!==-1){o+=q.slice(r+1)}}}var p=this.deferred.register();i.request({type:"GET",url:o,success:function(s){n.options=s;n._buildForm();n.message.update({status:"success",message:"Now you are using '"+n.options.name+"' version "+n.options.version+".",persistent:false});n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(s)},error:function(s){n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(s);var t=s.error||"Uncaught error.";n.modal.show({title:"Tool cannot be executed",body:t,buttons:{Close:function(){n.modal.hide()}}})}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(s){if(s.values.length>0&&s.values[0]&&s.values[0].src==="hda"){return n.content.get({id:s.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function r(v){for(var t in n.input_list){var u=n.field_list[t];var s=n.input_list[t];if(s.is_dynamic&&u.wait&&u.unwait){if(v){u.wait()}else{u.unwait()}}}}r(true);var q=this.deferred.register();var p=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;i.request({type:"GET",url:p,data:o,success:function(s){n._updateForm(s);r(false);n.deferred.done(q);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(s)},error:function(s){n.deferred.done(q);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(s)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(!_.isEqual(p.options,u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];if((["data","data_collection","drill_down"]).indexOf(p.type)!=-1){t=p.options}else{for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(){var x=this;this.field_list={};this.input_list={};this.element_list={};this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);var y=this.options;this.message=new m.Message();var n="This tool requires ";for(var r in y.requirements){var w=y.requirements[r];n+=w.name;if(w.version){n+=" (Version "+w.version+")"}if(r<y.requirements.length-2){n+=", "}if(r==y.requirements.length-2){n+=" and "}}n+=".";var t=new m.ButtonIcon({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;x.message.update({persistent:true,message:n,status:"warning"})}else{this.visible=false;x.message.update({message:""})}}});if(!y.requirements||y.requirements.length==0){t.$el.hide()}var p=new m.ButtonMenu({icon:"fa-cubes",title:"Versions",tooltip:"Select another tool version"});if(y.versions&&y.versions.length>1){for(var r in y.versions){var u=y.versions[r];if(u!=y.version){p.addMenu({title:"Switch to "+u,version:u,icon:"fa-cube",onclick:function(){y.id=y.id.replace(y.version,this.version);y.version=this.version;x.deferred.reset();x.deferred.execute(function(){x._buildModel()})}})}}}else{p.$el.hide()}var s=new m.ButtonMenu({icon:"fa-gear",title:"Options",tooltip:"View available options"});if(y.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(y.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(y.biostar_url+"/t/"+y.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+y.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+y.id+"/download"}})}this.section=new l.View(x,{inputs:y.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+y.name+"</b> "+y.description+" (Version "+y.version+")",cls:"ui-portlet-slim",operations:{requirements:t,menu:s,versions:p},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute: "+y.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){x.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(y.help!=""){this.$el.append(d.help(y.help))}if(y.citations){var v=$("<div/>");var o=new k.ToolCitationCollection();o.tool_id=y.id;var q=new a.CitationListView({el:v,collection:o});q.render();o.fetch();this.$el.append(v)}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.rebuild();if(y.message){this.message.update({persistent:true,status:"warning",message:y.message})}this._showErrors(y)},_showErrors:function(o){if(o.errors){this.tree.finalize();var p=this.tree.matchResponse(o.errors);for(var n in p){this.foundError(n,p[n],true)}}},foundError:function(o,p,n){var q=this.element_list[o];q.error(p||"Please verify this parameter.");if(!n){$(this.container).animate({scrollTop:q.$el.offset().top-20},500)}}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var o=parent.Galaxy;if(o&&o.modal){this.modal=o.modal}else{this.modal=new m.Modal.View()}if(o&&o.currUser){this.is_admin=o.currUser.get("is_admin")}else{this.is_admin=false}this.options=n;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(n){$(this.container).empty();$(this.container).append(n)},highlight:function(o,p,n){var q=this.element_list[o];if(q){q.error(p||"Please verify this parameter.");if(!n){$(this.container).animate({scrollTop:q.$el.offset().top-20},500)}}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{o+="tool_version="+this.options.version+"&";var q=top.location.href;var r=q.indexOf("?");if(q.indexOf("tool_id=")!=-1&&r!==-1){o+=q.slice(r+1)}}}var p=this.deferred.register();i.request({type:"GET",url:o,success:function(s){n.options=s;n._buildForm();n.message.update({status:"success",message:"Now you are using '"+n.options.name+"' version "+n.options.version+".",persistent:false});n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(s)},error:function(s){n.deferred.done(p);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(s);var t=s.error||"Uncaught error.";n.modal.show({title:"Tool cannot be executed",body:t,buttons:{Close:function(){n.modal.hide()}}})}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(s){if(s.values.length>0&&s.values[0]&&s.values[0].src==="hda"){return n.content.get({id:s.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function r(v){for(var t in n.input_list){var u=n.field_list[t];var s=n.input_list[t];if(s.is_dynamic&&u.wait&&u.unwait){if(v){u.wait()}else{u.unwait()}}}}r(true);var q=this.deferred.register();var p=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;i.request({type:"GET",url:p,data:o,success:function(s){n.tree.matchModel(s,function(u,y){var t=n.input_list[u];if(t&&t.options){if(!_.isEqual(t.options,y.options)){t.options=y.options;var z=n.field_list[u];if(z.update){var x=[];if((["data","data_collection","drill_down"]).indexOf(t.type)!=-1){x=t.options}else{for(var w in y.options){var v=y.options[w];if(v.length>2){x.push({label:v[0],value:v[1]})}}}z.update(x);z.trigger("change");console.debug("Updating options for "+u)}}}});r(false);n.deferred.done(q);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(s)},error:function(s){n.deferred.done(q);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(s)}})},_buildForm:function(){var n=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);var p=this.options;this._renderForm(p);this.tree.finalize();if(p.errors){var q=this.tree.matchResponse(p.errors);for(var o in q){this.highlight(o,q[o],true)}}this.on("refresh",function(){n.deferred.reset();n.deferred.execute(function(){n._updateModel()})});this.on("reset",function(){for(var r in this.element_list){this.element_list[r].reset()}})},_renderForm:function(y){var x=this;this.message=new m.Message();var n="This tool requires ";for(var r in y.requirements){var w=y.requirements[r];n+=w.name;if(w.version){n+=" (Version "+w.version+")"}if(r<y.requirements.length-2){n+=", "}if(r==y.requirements.length-2){n+=" and "}}n+=".";var t=new m.ButtonIcon({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;x.message.update({persistent:true,message:n,status:"warning"})}else{this.visible=false;x.message.update({message:""})}}});if(!y.requirements||y.requirements.length==0){t.$el.hide()}var p=new m.ButtonMenu({icon:"fa-cubes",title:"Versions",tooltip:"Select another tool version"});if(y.versions&&y.versions.length>1){for(var r in y.versions){var u=y.versions[r];if(u!=y.version){p.addMenu({title:"Switch to "+u,version:u,icon:"fa-cube",onclick:function(){y.id=y.id.replace(y.version,this.version);y.version=this.version;x.deferred.reset();x.deferred.execute(function(){x._buildModel()})}})}}}else{p.$el.hide()}var s=new m.ButtonMenu({icon:"fa-gear",title:"Options",tooltip:"View available options"});if(y.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(y.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(y.biostar_url+"/t/"+y.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+y.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+y.id+"/download"}})}this.section=new l.View(x,{inputs:y.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+y.name+"</b> "+y.description+" (Version "+y.version+")",cls:"ui-portlet-slim",operations:{requirements:t,menu:s,versions:p},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute: "+y.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){x.job_handler.submit()}})}});this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(y.help!=""){this.$el.append(d.help(y.help))}if(y.citations){var v=$("<div/>");var o=new k.ToolCitationCollection();o.tool_id=y.id;var q=new a.CitationListView({el:v,collection:o});q.render();o.fetch();this.$el.append(v)}if(y.message){this.message.update({persistent:true,status:"warning",message:y.message})}}});return{View:b}}); \ No newline at end of file diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.refresh()}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.trigger("refresh")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac 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(c){this.app=c},submit:function(){var c=this;var d={tool_id:this.app.options.id,tool_version:this.app.options.version,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.reciept(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.app.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()}}})}}})},_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.app.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.app.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.app.foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");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(c){this.app=c},submit:function(){var c=this;var d={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("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.reciept(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.app.highlight(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()}}})}}})},_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.app.highlight(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.app.highlight(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.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_collection":i=this._fieldData(h);break;case"data_column":h.error_text="Missing columns in referenced dataset.";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.trigger("refresh")};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.trigger("refresh")}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.trigger("refresh")}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_collection":i=this._fieldData(h);break;case"data_column":h.error_text="Missing columns in referenced dataset.";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.trigger("refresh")}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.trigger("refresh")}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.trigger("refresh")}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.trigger("refresh")}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r 17933aef1d3527d22211ff7bf0e47bbbac66c4ac static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){if(q.optional&&p.validate&&!p.validate()){r=null}c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},finalize:function(f){var a=this;this.map_dict={};if(!this.app.section){return{}}f=f||{};var e={};var d={};this._iterate(this.app.section.$el,d);function c(i,h,g){e[i]=g;a.map_dict[i]=h}function b(n,q){for(var l in q){var j=q[l];if(j.input){var s=j.input;var m=n;if(n!=""){m+="|"}m+=s.name;switch(s.type){case"repeat":var h="section-";var v=[];var p=null;for(var u in j){var o=u.indexOf(h);if(o!=-1){o+=h.length;v.push(parseInt(u.substr(o)));if(!p){p=u.substr(0,o)}}}v.sort(function(w,i){return w-i});var l=0;for(var k in v){b(m+"_"+l++,j[p+v[k]])}break;case"conditional":var t=a.app.field_list[s.id].value();if(f[s.test_param.type]){t=f[s.test_param.type](t)}c(m+"|"+s.test_param.name,s.id,t);var g=a.matchCase(s,t);if(g!=-1){b(m,q[s.id+"-section-"+g])}break;default:var r=a.app.field_list[s.id];var t=r.value();if(f[s.type]){t=f[s.type](t)}if(!r.skip){if(s.optional&&r.validate&&!r.validate()){t=null}c(m,s.id,t)}}}}}b("",d);return e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.map_dict[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.map_dict[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},_iterate:function(c,d){var a=this;var b=$(c).children();b.each(function(){var g=this;var f=$(g).attr("id");if($(g).hasClass("section-row")){d[f]={};var e=a.app.input_list[f];if(e){d[f]={input:e}}a._iterate(g,d[f])}else{a._iterate(g,d)}})}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0