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webclient.js-i2b2.cells.plugins.community.CAREobsTally.assets.injected_screens.html Maven / Gradle / Ivy

	
		

			

				

					
Specify Data
					
Output Options
					
View Results
					
Export Data
					
Plugin Help
				
				

					

						

							

								

									Drop a patient set and a concept (ontology term) onto the appropriate input boxes below, then click the "Output Options" tab to specify layout of the resulting data, before clicking on the "View Results" tab to retrieve the demographic comparison of the cohort subsets that are associated with the selected observation counts of the specified concept 


									For more information, refer to the "Plugin Help" tab.


								
 
								
 

								
Patient Set:
								
Drop a Patient Set here
								

									

										Starting Patient:
										   Number of Patients:
										  
										
											HELP
										
										
Query Subgroup Size:
										  
										HELP
									
								

								
Concept:
								

									
Drop a Concept here
								
								

									  HINT
								
						
							
						
					
					

						

							

								

									Select the appropriate grouping of observation tallies against which to generate the resulting histograms below.


									For more information, refer to the "Plugin Help" tab.


								
 
								

								

									
Group observation tallies in sequence of '1, 2, 3, 4, 5, 6, 7, 8, 9, over 9'
									
Group observation tallies in sequence of '1, 2, 3, 4, 5, over 5'
									
Group observation tallies in sequence of '1-2, 3-4, 5-6, 7-8, over 8'
									
Group observation tallies in sequence of '1-3, 4-6, 7-9, over 9'
									
Group observation tallies in sequence of '1-5, 6-10, over 10'
									


								
								

								

									
Next, click on the "View Results" tab to retrieve the demographic comparison of the cohort subsets that are associated with the selected observation counts of the specified concept.
								
 
							
						
					
					

						

							
Please specify a Patient Set and a Concept at the "Specify Data" tab, as well as select the appropriate grouping of observation tallies against which to generate the resulting histograms at the "Output Options" tab, first.
							

								In progress...
								

Retrieving data, from the server (i2b2 hive), to create the histograms.
								


								

								


								

								


								

Please wait ...

								





							
							

							

							  

							  

Warning: The server (i2b2 hive) has returned an error -- apparently, it has been overwhelmed by the amount of data requested of it, and had failed!!
							  

Unfortunately, this server failure has also left this current webclient session in a bad state!!
							  

Please logout of this webclient session (to allow the flushing of remnants of this server failure, in certain occasions, it may even be necessary to close the current web browser) and login to a new webclient session.  Then start this webclient plugin again, and reduce either the 'Number of Patients' or 'Query Subgroup Size' (to a smaller non-zero value), or both, in the "Specify Data" tab.
							
						
					
					

						

							
Please specify a Patient Set and a Concept at the "Specify Data" tab; then select the appropriate grouping of observation tallies against which to generate the resulting histograms at the "Output Options" tab; as well as review the resulting histograms at the "View Results" tab; repectively, first.
							

								

									

										

										Click on one of the buttons to download the data of the histograms, of the "View Results" tab, in the desired format, onto your computer.
									
									

									

										


											

												
												
											
	
										
	
										

											This initiates the download of an 'i2b2-export_CARE-obsTally_[timestamp].csv' file.
											
										
									
									

									

										


											

												
												
											
	
										
										
										

											This initiates the download of an 'i2b2-export_CARE-obsTally_[timestamp].html.xls' file, which can be readily openned with MS Excel.
											
											  

												
MS Excel may launch a warning message when the file is loaded; simply click 'Yes' to proceed.
												
To open it in a web browser instead, simply remove the '.xls' file extension, to allow the '.html' extension take effect.
											  
											  
										
									
								
							
						
					
					

						

							

								
Introduction
								This plugin provides the following functions:
								

								  
Generates demographic histograms on the subsets of patients associated (observed) with any various counts of observations of a selected concept (ontology term).
								  
Allows the usage of smaller queries of patient subgroups (from a large patient set) iteratively, in place of one single large query of that huge patient set, to reduce risk of overwhelming the server (i2b2 hive).
								  
Allows selection of subset of patients from a large patient set, to further reduce risk of overwhelming the server.
								  
Allows selection of the appropriate grouping of observation tallies against which to generate the resulting histograms.
								  
Provides feedbacks on current progress, elapsed time, and estimated remaining run time.
								  
Provides notification & suggestion in cases of paging (query-subgrouping) by the server.
								  
Provides termination indication & suggestion (for recovery) when the server failed.
								  
Provides detailed 'HELP' and 'HINT' dialogs in response to corresponding hotlinks strategically placed next to input fields that may need explanations or suggestion.
								  
Provides options to export histogram data into a CSV or XLS file that can easily be used by MS Excel, SPSS and other statistics software.
								
								

								
Instructions
								

								  
Navigate to the "Specify Data" tab. Drag and drop a Patient Set and a concept (ontology term) onto the appropriate input boxes:
									

									  
Enter appropriate values in the 'Starting Patient' and 'Number of Patients' fields that are then presented, to specify the subset of the patient set to use.  Also specify at the 'Query Subgroup Size' field the size of smaller queries of subgroups of patients to be used iteratively, to facilitate reducing the risks of overwhelming the server (i2b2 hive).
									  
Click on the corresponding 'HELP' hotlinks next to the 'Starting Patient' and 'Number of Patients' fields, and the 'HELP' hotlink next to the 'Query Subgroup Size' field, for detailed information; and enter corresponding appropriate values.
									  
Click on the corresponding 'HINT' hotlink below the 'Concepts' field for hint or suggestion for selecting concepts.
									
								  
								  
Next, select the appropriate grouping of observation tallies against which to generate the resulting histograms at the "Output Options" tab
								  
								  
Then, select the "View Results" tab to wait for and view the generated demographic histograms.
								  
								  
Finally, select the "Export Data" tab to click the appropriate button to download the histogram data, in the desired form, to the local computer.
								  
								
								

								
Caveats
								

								  
Since it is possible for the server (i2b2 hive) to take a long time to provide all the data requested, this plugin provides occasional updates of 'Elapsed time' and 'estimated remaining run time', etc. displays while the data are being fetched.  These displayed values are at best rough estimates based on occasional data coming back from the server.  In the case of zero 'Query Subgroup Size' selected (i.e. no query-subgrouping), then there would be no data coming back from the server until either of the following situations:
									

										
The whole, single, query is done.
										
The server itself started paging (i.e. query-subgrouping), and the result of the 1st of such paged subqueries just arrived.
										
The server got overwhelmed by all the excessive data and failed, returning an 'error'.
									
								  In any of these cases, the updates of 'Elapsed time' and 'estimated remaining run time' will be quite infrequent, as updates from the server (i2b2 hive) will most likely take a long time, and far and few in-between, if any.
   								  
This plugin also tries to provide updates on the current subgroup the server (i2b2 hive) is fetching. However, in the cases when the server (i2b2 hive) itself started paging (i.e. query-subgrouping), then the current subgroup # being fetched may exceed the original stated total number of subgroups.
								  
The exact behaviors of exporting data in the desired files will be different among the various browsers (Firefox, Chrome, Internet Explorer, Safari, and Opera).  Most of these browsers will present options between saving and just opening the exported file; while certain browsers, like Internet Explorer, may also open up a new blank tab page along with the export action.
								
								

								
Browser Compatibilities
								

								  
This plugin has been successfully tested with the following browsers: Firefox (v31, v35), Chrome (v41), Internet Explorer 32/64 (v10, v11), Safari (v5.1.7), and Opera (v28); all on Windows 7.
								  
Its "Export Data" feature does not work with Vivaldi (v1.0.94.2).
								  
The i2b2 web client itself does not work with Opera (v12.11, v12.16).
								
								

								
i2b2 version compatibilities
								This current version is compatible with i2b2 v.1.6-1.7.
								

								
Version History
								

								 

								  
1.0
								  

								   Initial release, with options to use a subset of a large patient set; selection of observation tallies grouping for resulting histograms; user-friendly feedback (estimated run-time, etc.), helps & hints.
By Wayne Chan, University of Massachusetts Medical School, Worcester, USA.
								  
								  
2015 Q1
 								 
								 

								  
1.1
								  

								   Added "Export Data" options & other minor refinements.
By Wayne Chan, University of Massachusetts Medical School, Worcester, USA.
								  
								  
2015 Q2
 								 
								 

								  
1.2
								  

								   Fixed compatibility issue with the prototype.js v.1.7.2 (ships with webclient v1.7.0.7), & other minor touch-ups.
By Wayne Chan.
								  
								  
2015 Q4
 								 
								
								

								
Terms of Use
								This plugin is published under the GNU GPL v3 license.
                                

  
								This software is distributed as a plugin to the i2b2 v1.6-1.7  webclient framework, and may be used free of charge.  It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
								PARTICULAR PURPOSE.