Changeset 25
- Timestamp:
- Mar 31, 2011, 12:07:02 PM (12 years ago)
- Location:
- trunk
- Files:
-
- 9 added
- 12 edited
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grails-app/conf/BaseFilters.groovy (modified) (1 diff)
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grails-app/controllers/nl/tno/metagenomics/files/FileController.groovy (modified) (3 diffs)
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grails-app/taglib/nl/tno/metagenomics/UploadTagLib.groovy (modified) (2 diffs)
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grails-app/views/assay/show.gsp (modified) (1 diff)
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grails-app/views/layouts/main.gsp (modified) (1 diff)
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grails-app/views/run/_addFilesDialog.gsp (modified) (1 diff)
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grails-app/views/run/index.gsp (modified) (1 diff)
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grails-app/views/run/show.gsp (modified) (1 diff)
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web-app/css/fileuploader.new.css (modified) (1 diff)
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web-app/css/metagenomics.css (modified) (2 diffs)
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web-app/js/addFilesDialog.js (modified) (1 diff)
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web-app/js/fileuploads.new.js (modified) (6 diffs)
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web-app/js/fileuploads.old.js (added)
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web-app/uploadify (added)
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web-app/uploadify/button.png (added)
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web-app/uploadify/cancel.png (added)
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web-app/uploadify/expressInstall.swf (added)
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web-app/uploadify/jquery.uploadify.v2.1.4.min.js (added)
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web-app/uploadify/swfobject.js (added)
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web-app/uploadify/uploadify.css (added)
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web-app/uploadify/uploadify.swf (added)
Legend:
- Unmodified
- Added
- Removed
-
trunk/grails-app/conf/BaseFilters.groovy
r20 r25 36 36 } 37 37 38 // File uploads don't occur in a session, since the flash script can't 39 // continue the session. For that reason, all uploads are allowed. 40 if( actionName == "upload" && controllerName == "file" ) { 41 return true; 42 } 43 38 44 if( !ConfigurationHolder.config.gscf.baseURL ) { 39 45 throw new Exception( "No GSCF instance specified. Please check configuration." ) -
trunk/grails-app/controllers/nl/tno/metagenomics/files/FileController.groovy
r22 r25 18 18 19 19 import org.codehaus.groovy.grails.commons.ConfigurationHolder 20 import org.springframework.web.multipart.MultipartHttpServletRequest 20 21 import grails.converters.* 21 22 import org.apache.commons.io.IOUtils; … … 180 181 181 182 protected def moveUploadedFile(File absolutePath ) { 182 PrintWriter writer = null; 183 InputStream is = null; 184 FileOutputStream fos = null; 185 186 try { 187 writer = response.getWriter(); 188 } catch (IOException ex) { 189 log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); 190 } 191 192 String filename = request.getHeader("X-File-Name"); 183 if( !( request instanceof MultipartHttpServletRequest ) ) { 184 response.setStatus( response.SC_BAD_REQUEST ); 185 log.error( "Request for file upload is not multipart: " + params ); 186 return []; 187 } 188 189 MultipartHttpServletRequest mpr = (MultipartHttpServletRequest) request; 190 def uploadedFile = mpr.getFile( 'Filedata' ) 191 192 String filename = uploadedFile.getOriginalFilename(); 193 193 194 194 // URL decode the filename … … 198 198 String newFilename = fileService.getUniqueFilename( filename, absolutePath ); 199 199 try { 200 is = request.getInputStream(); 201 fos = new FileOutputStream(new File(absolutePath, newFilename)); 202 IOUtils.copy(is, fos); 200 uploadedFile.transferTo( new File( absolutePath, newFilename ) ); 201 203 202 response.setStatus(response.SC_OK); 203 204 204 return [ 'success': true, 'filename': newFilename ] 205 } catch (FileNotFoundException ex) { 205 } catch (Exception ex) { 206 log.error( "Fileupload has thrown an exception: " + ex.getMessage()); 207 206 208 response.setStatus(response.SC_INTERNAL_SERVER_ERROR); 207 log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage());208 209 209 return [ 'success': false ] 210 } catch (IOException ex) {211 response.setStatus(response.SC_INTERNAL_SERVER_ERROR);212 log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage());213 214 return [ 'success': false ]215 } finally {216 try {217 fos.close();218 is.close();219 } catch (IOException ignored) {220 }221 210 } 222 211 } -
trunk/grails-app/taglib/nl/tno/metagenomics/UploadTagLib.groovy
r9 r25 15 15 def fileUpload = { attrs -> 16 16 def multiple = attrs.multiple ?: false; 17 18 out << '<div id="upload_field_container_' + attrs.name + '" class="upload_field_container upload_field_container_' + ( multiple ? 'multiple' : 'single' ) + '">'; 19 out << '<div id="upload_field_' + attrs.name + '" class="upload_field"></div>'; 17 out << '<div class="uploadContainer" id="uploadcontainer_' + attrs.name + '">' 18 out << '<div class="files">' 20 19 out << '<div id="' + attrs.name + 'Example" class="upload_info"></div>'; 21 20 out << '<a id="' + attrs.name + 'DeleteExisting" class="upload_del" href="#" onClick="if( confirm( \'Are you sure to delete this file?\' ) ) { deleteFileExisting( \'' + attrs.name + '\' ); } return false;"><img src="' + resource( dir: 'images/icons', file: 'delete.png', plugin: 'famfamfam' ) + '"></a>'; 22 21 out << '<a id="' + attrs.name + 'DeleteUploaded" class="upload_del" href="#" onClick="if( confirm( \'Are you sure to delete this file?\' ) ) { deleteFileUploaded( \'' + attrs.name + '\' ); } return false;"><img src="' + resource( dir: 'images/icons', file: 'delete.png', plugin: 'famfamfam' ) + '"></a>'; 22 out << '</div>' 23 out << '<input type="file" name="ajaxupload_' + attrs.name + '" id="upload_field_' + attrs.name + '" />' 23 24 out << '<script type="text/javascript">'; 24 out << ' $( document).ready(function() { ';25 out << ' $(function() { '; 25 26 out << ' var filename = "' + ( attrs.value ?: '' ) + '";'; 26 27 out << ' fileUploadField( "' + attrs.name + '", ' + ( multiple ? 'true' : 'false' ) + ( attrs.onUpload ? ', function(params) { ' + attrs.onUpload + '(params); }' : '' ) + ( attrs.onDelete ? ', function(params) { ' + attrs.onDelete + '(params); }' : '' ) + ');'; 27 28 out << ' if( filename != "" ) {'; 28 29 out << ' $("#' + attrs.name + 'DeleteExisting").show();'; 29 out << ' $("#' + attrs.name + 'Example").html("Current file: " + createFileHTML( filename ) )'; 30 out << ' $("#' + attrs.name + 'Example").html("Current file: " + createFileHTML( filename ) );'; 31 out << ' $("#uploadcontainer_' + attrs.name + ' .files").show();'; 30 32 out << ' }'; 31 33 out << ' } );'; 32 34 out << "</script>\n"; 33 35 34 36 // Show a custom list when uploading multiple files 35 37 if( multiple ) { 36 out << '<ul class=" multipleFiles"></ul>';38 out << '<ul class="files"></ul>'; 37 39 } else { 38 40 out << '<input type="hidden" name="' + attrs.name + '" id="' + attrs.name + '" value="' + attrs.value + '">'; … … 40 42 41 43 out << '</div>'; 44 42 45 } 46 47 // def fileUpload = { attrs -> 48 // def multiple = attrs.multiple ?: false; 49 // 50 // out << '<div id="upload_field_container_' + attrs.name + '" class="upload_field_container upload_field_container_' + ( multiple ? 'multiple' : 'single' ) + '">'; 51 // out << '<div id="upload_field_' + attrs.name + '" class="upload_field"></div>'; 52 // out << '<div id="' + attrs.name + 'Example" class="upload_info"></div>'; 53 // out << '<a id="' + attrs.name + 'DeleteExisting" class="upload_del" href="#" onClick="if( confirm( \'Are you sure to delete this file?\' ) ) { deleteFileExisting( \'' + attrs.name + '\' ); } return false;"><img src="' + resource( dir: 'images/icons', file: 'delete.png', plugin: 'famfamfam' ) + '"></a>'; 54 // out << '<a id="' + attrs.name + 'DeleteUploaded" class="upload_del" href="#" onClick="if( confirm( \'Are you sure to delete this file?\' ) ) { deleteFileUploaded( \'' + attrs.name + '\' ); } return false;"><img src="' + resource( dir: 'images/icons', file: 'delete.png', plugin: 'famfamfam' ) + '"></a>'; 55 // out << '<script type="text/javascript">'; 56 // out << ' $(document).ready( function() { '; 57 // out << ' var filename = "' + ( attrs.value ?: '' ) + '";'; 58 // out << ' fileUploadField( "' + attrs.name + '", ' + ( multiple ? 'true' : 'false' ) + ( attrs.onUpload ? ', function(params) { ' + attrs.onUpload + '(params); }' : '' ) + ( attrs.onDelete ? ', function(params) { ' + attrs.onDelete + '(params); }' : '' ) + ');'; 59 // out << ' if( filename != "" ) {'; 60 // out << ' $("#' + attrs.name + 'DeleteExisting").show();'; 61 // out << ' $("#' + attrs.name + 'Example").html("Current file: " + createFileHTML( filename ) )'; 62 // out << ' }'; 63 // out << ' } );'; 64 // out << "</script>\n"; 65 // 66 // // Show a custom list when uploading multiple files 67 // if( multiple ) { 68 // out << '<ul class="multipleFiles"></ul>'; 69 // } else { 70 // out << '<input type="hidden" name="' + attrs.name + '" id="' + attrs.name + '" value="' + attrs.value + '">'; 71 // } 72 // 73 // out << '</div>'; 74 // } 43 75 44 76 /** -
trunk/grails-app/views/assay/show.gsp
r24 r25 16 16 <g:javascript src="enterTagsDialog.js" /> 17 17 18 <g:javascript src="fileuploader.new.js" />19 18 <g:javascript src="fileuploads.new.js" /> 20 19 -
trunk/grails-app/views/layouts/main.gsp
r15 r25 22 22 <script type="text/javascript" src="${resource(dir: 'js', file: 'paginate.js')}"></script> 23 23 <script type="text/javascript" src="${resource(dir: 'js', file: 'forms.js')}"></script> 24 25 <!-- Uploadify --> 26 <link href="${resource(dir: 'uploadify', file: 'uploadify.css')}" type="text/css" rel="stylesheet" /> 27 <script type="text/javascript" src="${resource(dir: 'uploadify', file: 'swfobject.js')}"></script> 28 <script type="text/javascript" src="${resource(dir: 'uploadify', file: 'jquery.uploadify.v2.1.4.min.js')}"></script> 24 29 25 30 <g:layoutHead/> -
trunk/grails-app/views/run/_addFilesDialog.gsp
r7 r25 7 7 Select sequence and quality files to upload. It is possible to zip the files before upload. 8 8 </p> 9 <g:fileUpload name="sequencefiles" value="" multiple="${true}" onUpload="handleFileUploadData" onDelete="deleteProcessButton" />9 <g:fileUpload name="sequencefiles" value="" multiple="${true}" onUpload="handleFileUploadData" onDelete="deleteProcessButton" /> 10 10 </g:form> 11 11 </div> -
trunk/grails-app/views/run/index.gsp
r18 r25 6 6 <g:javascript src="run.index.runDialog.js" /> 7 7 8 <g:javascript src="fileuploader.new.js" />9 8 <g:javascript src="fileuploads.new.js" /> 10 9 -
trunk/grails-app/views/run/show.gsp
r24 r25 19 19 <g:javascript src="assay.show.showRunDialog.js" /> 20 20 21 <g:javascript src="fileuploader.new.js" />22 21 <g:javascript src="fileuploads.new.js" /> 23 22 -
trunk/web-app/css/fileuploader.new.css
r2 r25 8 8 .upload_field_container .qq-upload-list { display: none; } 9 9 10 .upload _field_container .multipleFiles { list-style-type: none; margin-left: 0; padding-left: 0; }11 .upload _field_container .multipleFiles li { margin: 3px 0px; border-bottom: 1px solid #ccc;}12 .upload _field_container .multipleFiles li:last-child { border-bottom-width: 0px; }13 .upload _field_container .multipleFiles li span {10 .uploadContainer ul.files { list-style-type: none; margin-left: 0; padding-left: 0; } 11 .uploadContainer ul.files li { margin: 2px 0px; border-bottom: 1px solid #ccc; } 12 .uploadContainer ul.files li:last-child { border-bottom-width: 0px; } 13 .uploadContainer ul.files li span { padding: 4px 0; 14 14 display: inline-block; 15 15 zoom: 1; /* IE 6 & 7 hack */ 16 16 *display: inline; /* IE 6 & 7 hack */ 17 17 } 18 .upload _field_container .multipleFiles li span.filename { width: 200px; margin-right: 10px; }19 .upload _field_container .multipleFiles li span.filesize { width: 60px; margin-right: 10px; }18 .uploadContainer ul.files li span.filename { width: 280px; margin-right: 10px; } 19 .uploadContainer ul.files li span.filesize { width: 60px; margin-right: 10px; } 20 20 21 21 .upload_info { color: #006DBA; display: inline; margin-left: 5px; } -
trunk/web-app/css/metagenomics.css
r24 r25 220 220 width: 120px; 221 221 display: inline-block; 222 vertical-align: top; 222 223 zoom: 1; /* IE 6 & 7 hack */ 223 224 *display: inline; /* IE 6 & 7 hack */ … … 496 497 .ui-dialog .assaySampleDetails span.value { width: 150px; display: inline-block; *display: inline; zoom: 1; } 497 498 499 .uploadContainer { display: inline-block; *display: inline; zoom: 1 } 500 498 501 /* Makes sure the filenames in the dialog don't exceed 200px */ 499 502 .dataTables_wrapper .uploadedFile { display: inline-block; zoom: 1; *display: inline; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; width: 190px; height: 15px; } -
trunk/web-app/js/addFilesDialog.js
r9 r25 36 36 */ 37 37 function deleteProcessButton( params ) { 38 if( $( '#upload_field_container_sequencefiles .multipleFiles li' ).size() == 0 ) {38 if( $( '#upload_field_container_sequencefiles ul.files li' ).size() == 0 ) { 39 39 var firstButton = $(":button:contains('Process')"); 40 40 firstButton.attr("disabled","disabled").addClass('ui-state-disabled'); -
trunk/web-app/js/fileuploads.new.js
r2 r25 1 // The uploadfields are saved in an array to avoid them being created twice in a jquery dialog 2 var uploadfields = new Array(); 3 1 4 /************************************************* 2 5 * … … 23 26 if( multiple == undefined ) 24 27 multiple = false; 28 29 // Check whether the field has already been created 30 if( uploadfields[ field_id ] != undefined ) 31 return; 25 32 26 33 var uploader; … … 30 37 uploader = _createSingleUploader( field_id, uploadCallback, deleteCallback ); 31 38 } 39 40 uploadfields[ field_id ] = uploader; 32 41 } 33 42 … … 45 54 */ 46 55 function _createSingleUploader( field_id, uploadCallback, deleteCallback ) { 47 var uploader; 48 uploader = new qq.FileUploader({ 49 element: document.getElementById( 'upload_field_' + field_id ), 50 action: baseUrl + '/file/upload', 51 params : {}, 52 name : field_id, 53 multiple: false, 54 onSubmit : function(id, file){ 55 oldFile = $('#' + field_id).val(); 56 if( oldFile != '' ) { 57 if( !confirm( 'The old file is deleted when uploading a new file. Do you want to continue?') ) { 58 return false; 56 var clearId = null; 57 $('#upload_field_' + field_id ).uploadify({ 58 'uploader' : baseUrl + '/uploadify/uploadify.swf', 59 'script' : baseUrl + '/file/upload', 60 'cancelImg' : baseUrl + '/uploadify/cancel.png', 61 'auto' : true, 62 'removeCompleted': true, 63 'multi' : false, 64 'height' : 20, 65 'buttonImg': baseUrl + '/uploadify/button.png', 66 'onSelect' : function(event, id, fileObj) { 67 var oldFile = $('#' + field_id).val(); 68 if( oldFile != '' ) { 69 if( !confirm( 'The old file is deleted when uploading a new file. Do you want to continue?') ) { 70 clearId = id; 71 return false; 72 } 73 74 // Delete the file from disk, if it has been just uploaded. If the file was already moved from 75 // the temporary directory, if will not be deleted 76 if( $('#' + field_id + 'DeleteUploaded').css( 'display' ) != 'none' ) { 77 deleteFileUploaded( field_id ); 78 } 79 $('#' + field_id + 'DeleteExisting').hide(); 80 $('#' + field_id + 'DeleteUploaded').hide(); 59 81 } 60 82 61 // Delete the file from disk, if it has been just uploaded. If the file was already moved from 62 // the temporary directory, if will not be deleted 63 if( $('#' + field_id + 'DeleteUploaded').css( 'display' ) != 'none' ) { 64 deleteFileUploaded( field_id ); 83 $('#upload_field_' + field_id ).uploadifySettings( 'scriptData', { 84 'field': field_id, 85 'oldFile': oldFile 86 }, true); 87 88 }, 89 'onSelectOnce': function( event, data ) { 90 // This is a hack to cancel upload if the user doesn't want to overwrite his already 91 // uploaded file. It should be possible to cancel an upload using 'return false' from 92 // the onSelect event, but that doesn't work. See also uploadify forums 93 if( clearId != null ) { 94 $('#upload_field_' + field_id ).uploadifyCancel( clearId ); 95 clearId = null; 96 } 97 }, 98 'onComplete' : function(event, id, file, response, data) { 99 // Parse as json 100 var responseJSON = JSON.parse( response ); 101 102 if( response == "" || !responseJSON.success ) { 103 $('#' + field_id).val( '' ); 104 $('#' + field_id + 'Example').html('<span class="error">Error uploading ' + createFileHTML( file.name ) + '</span>' ); 105 $('#' + field_id + 'DeleteUploaded').hide(); 106 } else { 107 // Activate user callback if supplied 108 if( typeof uploadCallback == 'function') 109 uploadCallback( {field: field_id, filename: responseJSON.filename} ); 110 111 $('#' + field_id).val( responseJSON.filename ); 112 113 $('#' + field_id + 'Example').html('Uploaded ' + createFileHTML( responseJSON.filename ) ); 114 $('#' + field_id + 'DeleteUploaded').show(); 115 $('#uploadcontainer_' + field_id + ' .files').show(); 65 116 } 66 117 } 67 68 uploader.setParams({ 69 'field': field_id, 70 'oldFile': oldFile 71 }); 72 73 // Give feedback to the user 74 $('#' + field_id + 'Example').html('Uploading ' + createFileHTML( file ) + ': ' + _createProgressHtml( field_id ) ); 75 $('#' + field_id + 'Progress').show(); 76 $('#' + field_id + 'DeleteExisting').hide(); 77 $('#' + field_id + 'DeleteUploaded').hide(); 78 79 return true; 80 }, 81 onProgress: function(id, fileName, loaded, total) { 82 if (loaded != total){ 83 text = Math.round(loaded / total * 100) + '% from ' + uploader._formatSize(total) + " " + _createSpinnerHtml(); 84 } else { 85 text = uploader._formatSize(total); 86 } 87 $('#' + field_id + 'Progress').html( text ); 88 }, 89 onComplete : function(id, file, responseJSON) { 90 if( responseJSON == "" || !responseJSON.success ) { 91 $('#' + field_id).val( '' ); 92 $('#' + field_id + 'Example').html('<span class="error">Error uploading ' + createFileHTML( file ) + '</span>' ); 93 $('#' + field_id + 'DeleteUploaded').hide(); 94 } else { 95 // Activate user callback if supplied 96 if( typeof uploadCallback == 'function') 97 uploadCallback( {field: field_id, filename: responseJSON.filename} ); 98 99 $('#' + field_id).val( responseJSON.filename ); 100 101 $('#' + field_id + 'Example').html('Uploaded ' + createFileHTML( responseJSON.filename ) ); 102 $('#' + field_id + 'DeleteUploaded').show(); 103 } 104 } 118 105 119 }); 106 120 … … 116 130 } 117 131 118 return uploader;132 return $('#upload_field_' + field_id ); 119 133 } 120 134 … … 133 147 */ 134 148 function _createMultipleUploader( field_id, uploadCallback, deleteCallback ) { 135 var uploader; 136 uploader = new qq.FileUploader({ 137 element: document.getElementById( 'upload_field_' + field_id ), 138 action: baseUrl + '/file/upload', 139 params : {}, 140 name : field_id, 141 multiple: true, 142 onSubmit : function(id, file){ 143 uploader.setParams({ 144 'field': field_id, 145 'oldFile': '' 146 }) 147 148 // Give feedback to the user 149 $('#' + field_id + 'Example').html('Uploading ' + createFileHTML( file ) + ': ' + _createProgressHtml( field_id ) ); 150 $('#' + field_id + 'Progress').show(); 151 152 return true; 153 }, 154 onProgress: function(id, fileName, loaded, total) { 155 if (loaded != total){ 156 text = Math.round(loaded / total * 100) + '% from ' + uploader._formatSize(total) + " " + _createSpinnerHtml(); 157 } else { 158 text = uploader._formatSize(total); 159 } 160 $('#' + field_id + 'Progress').html( text ); 161 }, 162 163 onComplete : function(id, file, responseJSON) { 164 if( responseJSON == "" || !responseJSON.success ) { 165 $('#' + field_id + 'Example').html('<span class="error">Error uploading ' + createFileHTML( file ) + '</span>' ); 166 } else { 167 // Activate user callback if supplied 168 if( typeof uploadCallback == 'function') 169 uploadCallback( {field: field_id, filename: responseJSON.filename} ); 170 171 // Add filename to the list 172 $( '#upload_field_container_' + field_id + ' ul.multipleFiles').append( _createMultipleFileHtml( field_id, id, responseJSON.filename, deleteCallback ) ); 173 174 // Remove progress text 175 $('#' + field_id + 'Example').text( '' ); 149 $('#upload_field_' + field_id ).uploadify({ 150 'uploader' : baseUrl + '/uploadify/uploadify.swf', 151 'script' : baseUrl + '/file/upload', 152 'cancelImg' : baseUrl + '/uploadify/cancel.png', 153 'auto' : true, 154 'removeCompleted': true, 155 'multi' : true, 156 'height' : 20, 157 'buttonImg': baseUrl + '/uploadify/button.png', 158 'onSelect' : function(event, id, fileObj) { 159 $('#upload_field_' + field_id ).uploadifySettings( 'scriptData', { 160 'field': field_id, 161 'oldFile': '' 162 }, true); 163 }, 164 'onComplete' : function(event, id, file, response, data) { 165 // Parse as json 166 var responseJSON = JSON.parse( response ); 167 168 if( response == "" || !responseJSON.success ) { 169 $('#' + field_id).val( '' ); 170 $('#' + field_id + 'Example').html('<span class="error">Error uploading ' + createFileHTML( file.name ) + '</span>' ); 171 } else { 172 // Activate user callback if supplied 173 if( typeof uploadCallback == 'function') 174 uploadCallback( {field: field_id, filename: responseJSON.filename} ); 175 176 //$('#' + field_id + 'Example').html('Uploaded ' + createFileHTML( responseJSON.filename ) ); 177 178 // Add filename to the list 179 $( '#uploadcontainer_' + field_id + ' ul.files').append( _createMultipleFileHtml( field_id, id, responseJSON.filename, deleteCallback ) ); 180 181 // Show the upload message and the files list 182 $('#uploadcontainer_' + field_id + ' .files').show(); 183 } 184 185 $( '#upload_field_' + field_id ).uploadifyCancel( id ); 176 186 } 177 }178 }); 179 return uploader;180 187 188 }); 189 190 return $('#upload_field_' + field_id ); 181 191 } 182 192
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