[galaxy-commits] commit/galaxy-central: jgoecks: HDA/LDDA models: synchronize them with 'data_type' and 'file_ext', properly fill data_type with Galaxy data types, and use file_ext in place of data_type throughput client code.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d152ed50547/ Changeset: 9d152ed50547 User: jgoecks Date: 2014-08-29 23:17:44 Summary: HDA/LDDA models: synchronize them with 'data_type' and 'file_ext', properly fill data_type with Galaxy data types, and use file_ext in place of data_type throughput client code. Affected #: 10 files diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2004,7 +2004,7 @@ history_content_type=hda.history_content_type, file_size = int( hda.get_size() ), update_time = hda.update_time.isoformat(), - data_type = hda.ext, + data_type = hda.datatype.__class__.__module__ + '.' + hda.datatype.__class__.__name__, genome_build = hda.dbkey, misc_info = hda.info.strip() if isinstance( hda.info, basestring ) else hda.info, misc_blurb = hda.blurb ) @@ -2316,7 +2316,8 @@ message = ldda.message, date_uploaded = ldda.create_time.isoformat(), file_size = int( ldda.get_size() ), - data_type = ldda.ext, + file_ext = ldda.ext, + data_type = ldda.datatype.__class__.__module__ + '.' + ldda.datatype.__class__.__name__, genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, @@ -2432,6 +2433,7 @@ file_size = int( ldda.get_size() ) except OSError: file_size = 0 + rval = dict( id = ldda.id, hda_ldda = 'ldda', model_class = self.__class__.__name__, @@ -2443,7 +2445,8 @@ file_size = file_size, file_name = ldda.file_name, update_time = ldda.update_time.isoformat(), - data_type = ldda.ext, + file_ext = ldda.ext, + data_type = ldda.datatype.__class__.__module__ + '.' + ldda.datatype.__class__.__name__, genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb ) diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -136,7 +136,7 @@ library_dataset_dict = content_item.to_dict() - return_item.update( dict( data_type=library_dataset_dict[ 'data_type' ], + return_item.update( dict( file_ext=library_dataset_dict[ 'file_ext' ], date_uploaded=library_dataset_dict[ 'date_uploaded' ], is_unrestricted=is_unrestricted, is_private=is_private, diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -344,7 +344,7 @@ genome_build: null, // data type - data_type : null, + file_ext : null, // backbone initialize initialize: function (options) { @@ -371,15 +371,15 @@ var metadata = model.get('metadata'); // check for datatype - if (!model.get('data_type')) { + if (!model.get('file_ext')) { return; } // get data type - this.data_type = model.get('data_type'); + this.file_ext = model.get('file_ext'); // check for bed-file format - if (this.data_type == 'bed') + if (this.file_ext == 'bed') { // verify that metadata exists if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol')) @@ -395,7 +395,7 @@ } // check for vcf-file format - if (this.data_type == 'vcf') + if (this.file_ext == 'vcf') { // search array function search (str, array) { diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/dataset/dataset-choice.js --- a/static/scripts/mvc/dataset/dataset-choice.js +++ b/static/scripts/mvc/dataset/dataset-choice.js @@ -75,7 +75,7 @@ * // returns a jQuery promise (that 'fail's only if no datasets are found matching 'where' below) * var choice = new DatasetChoiceModal( datasetJSON, { * datasetsOnly : false, - * where : { state: 'ok', data_type: 'bed', ... }, + * where : { state: 'ok', file_ext: 'bed', ... }, * multiselect : true, * selected : [ 'df7a1f0c02a5b08e', 'abcdef0123456789' ] * @@ -191,7 +191,7 @@ * Options: * datasetJSON: array of plain json objects representing allowed choices * datasetsOnly: T: only show datasets in the allowed choices, F: datasets + collections - * where: map of attributes to filter datasetJSON by (e.g. { data_type: 'bed' }) + * where: map of attributes to filter datasetJSON by (e.g. { file_ext: 'bed' }) * label: the label/prompt displayed * selected: array of dataset ids that will show as already selected in the control * @@ -263,7 +263,7 @@ '<span class="title"><%= selected.hid %>: <%= selected.name %></span>', '<span class="subtitle">', '<i><%= selected.misc_blurb %></i>', - '<i>', _l( 'format' ) + ': ', '<%= selected.data_type %></i>', + '<i>', _l( 'format' ) + ': ', '<%= selected.file_ext %></i>', '<i><%= selected.misc_info %></i>', '</span>', '</div>' @@ -355,7 +355,7 @@ * Additional options: * showHeaders: T: show headers for selected dataset attributes in the display table * cells: map of attribute keys -> Human readable/localized column headers - * (e.g. { data_type: _l( 'Format' ) }) - defaults are listed below + * (e.g. { file_ext: _l( 'Format' ) }) - defaults are listed below */ var MultiDatasetChoice = DatasetChoice.extend({ @@ -366,7 +366,7 @@ hid : _l( 'History #' ), name : _l( 'Name' ), misc_blurb : _l( 'Summary' ), - data_type : _l( 'Format' ), + file_ext : _l( 'Format' ), genome_build : _l( 'Genome' ), tags : _l( 'Tags' ), annotation : _l( 'Annotation' ) diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -413,10 +413,10 @@ '</div>', '<% } %>', - '<% if( dataset.data_type ){ %>', + '<% if( dataset.file_ext ){ %>', '<div class="datatype">', '<label class="prompt">', _l( 'format' ), '</label>', - '<span class="value"><%- dataset.data_type %></span>', + '<span class="value"><%- dataset.file_ext %></span>', '</div>', '<% } %>', diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -541,10 +541,10 @@ tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); tmpl_array.push(' </tr>'); - tmpl_array.push(' <% if (item.get("data_type")) { %>'); + tmpl_array.push(' <% if (item.get("file_ext")) { %>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' <td><%= _.escape(item.get("file_ext")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% } %>'); @@ -681,10 +681,10 @@ tmpl_array.push(' <td><%= _.escape(ldda.get("name")) %></td>'); tmpl_array.push(' </tr>'); - tmpl_array.push(' <% if (ldda.get("data_type")) { %>'); + tmpl_array.push(' <% if (ldda.get("file_ext")) { %>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(ldda.get("data_type")) %></td>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% } %>'); @@ -811,7 +811,7 @@ tmpl_array.push(' </tr>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' <td><%= _.escape(item.get("file_ext")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Genome build</th>'); diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/library/library-folder-view.js --- a/static/scripts/mvc/library/library-folder-view.js +++ b/static/scripts/mvc/library/library-folder-view.js @@ -232,10 +232,10 @@ tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); tmpl_array.push(' </tr>'); - tmpl_array.push(' <% if (item.get("data_type")) { %>'); + tmpl_array.push(' <% if (item.get("file_ext")) { %>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' <td><%= _.escape(item.get("file_ext")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% } %>'); diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -106,7 +106,7 @@ tmpl_array.push(' </td>'); tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset - tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("file_ext")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated tmpl_array.push(' <td>'); @@ -129,7 +129,7 @@ tmpl_array.push(' </td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>'); // dataset - tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("file_ext")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>'); diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/library/library-library-view.js --- a/static/scripts/mvc/library/library-library-view.js +++ b/static/scripts/mvc/library/library-library-view.js @@ -266,10 +266,10 @@ tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); tmpl_array.push(' </tr>'); - tmpl_array.push(' <% if (item.get("data_type")) { %>'); + tmpl_array.push(' <% if (item.get("file_ext")) { %>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' <td><%= _.escape(item.get("file_ext")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% } %>'); diff -r d44794f40ca5c4cb265f0c648b2a11622cf4c144 -r 9d152ed50547ced4aa961542a1c45cc14a974dce static/scripts/mvc/tools/tools-datasets.js --- a/static/scripts/mvc/tools/tools-datasets.js +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -30,7 +30,7 @@ return this.currHistoryContents.filter( function( content ){ // link details var history_content_type = content.get( 'history_content_type' ); - var data_type = content.get( 'data_type'); + var data_type = content.get( 'file_ext'); // apply filter return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === ''); 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