Creating user friendly web interfaces for R scripts automatically
Contents
1. button Please note this will only work for webapps installed on Linux Unix servers It won t work for webapps installed on Windows servers 22 9 15 Installing the application you have created Once the application has been created a link will appear on the final web page If you named the application for example myapp then the link will be called myapp tgz A link to an identical zipped copy called myapp zip is also provided Download one of these compressed files to a download directory and uncompress it eg tar zxvf myapp tgz If you called your application myapp then uncompressing produces a directory named myapp in your download directory containing a number of subdirectories build doc object web deploy lib src In order to use the application that you have created you just need to copy the war file from the deploy subdirectory to your Tomcat webapps directory eg On Unix systems cp _ download directory myapp deploy myapp war _ tomcat home webapps After a moment the server will automatically unpack the myapp war file for you creating a directory named myapp in Tomcat s webapps directory Then the application should be accessible from your browser at the URL http localhost 8080 myapp 10 Application description file If you called your application for example myapp then the application description file will be called myapp xml and will be found in the2. error txt The web application checks this file when the R script terminates and if it is not empty displays the message it contains on the web page If you want to include error checking code in your R script you could communicate error messages to the user of the application by way of the error txt file To do this simply include lines in your R script that write the error messages to the file error txt You need to include lines such as write The data file you submitted is in the wrong format file error txt q save no If the file error txt is not empty then the returning web page will not display any results that the R script may have produced prior to the error occurring 27 Warning messages from the R script can be communicated to the user by having the R script write warning messages to a file called warning txt The contents of this file will be displayed on the returning web page Unlike error messages if the file warning txt is not empty then the returning web page will still display any results that the R script may have produced 17 Browser Navigation Buttons You should not use the Browser navigation buttons i e Back Forward or Reload to navigate through Rwui You should use the buttons provided on the web pages to navigate through Rwui If you inadvertently do press one of the Browser navigation buttons a warning should popup giving you the option to cancel the reques
3. gt Preferences gt Advanced gt Scripts and Plugins and tick Enable Javascript for Navigator at the top In IE go to Tools Internet Options Security Custom Level scroll down to Scripting Advance Scripting and tick Enable You can specify the default size in pixels of the popup window in which the process information appears You can also specify the refresh rate in seconds for the message in the popup window The default refresh rate is every 5 seconds In addition to or instead of a text process information box the application can also display a graphical process information box This might be useful for example for showing users graphically the convergence of an iterative calculation Your R script must write the periodically updated graph for example at each iteration to a file called process_graph jpg 9 10 Upload R script Upload the R script 19 9 11 Upload subsidiary files On this page you can upload any subsidiary R scripts and or reference data sets They will be automat ically incorporated into the application in the correct location You can then access each one in your R script using the R variable name you are asked to provide on this page For example if you upload a subsidiary R script my subsidiary_script R and provide the R variable name subsid_script then you could use this subsidiary script in the main R script
4. height 5 res 100 pointsize 8 dev off 4 File upload size The size of file that can be uploaded in an application created by Rwui is limited to around 100Mb Upload fails for larger files without an error message The solution is to add this line towards the end of the file tomcat_home webapps your_app WEB INF struts config xml lt controller processorClass org apache struts action RequestProcessor maxFileSize 1G gt So that the end of the file will now look like this lt message resources parameter sreg ApplicationSettings null false 28 key settings gt lt controller processorClass org apache struts action RequestProcessor maxFileSize 1G gt lt struts config gt This will allow up to 1Gigabyte files to be uploaded if you want users to be able to upload up to 2Gigabytes then replace the 1G in the new line with 2G 5 Setting environment variables Linux Unix If the R script requires environment variables to be set for example for database access one way is to add export statements prior to the line R CMD BATCH in the file sremd sh which can be found at tomcat_home webapps your_app WEB INF sremd sh 19 Acknowledgments Our thanks to the developers at the Apache Software Foundation for Struts Tomcat and Ant to the developers at the R Foundation for R to the developers of the Google Maps API to the developers of the Java package XStream and to Romain Guay for the Java class S
5. R script so the following paragraphs provides the information you will need in case you do have to do this If for example your main R script runs additional R scripts using the source function in R You will need to place these additional R scripts somewhere accessible on the server and include the path to them when using the source command in your R script This could be the absolute path Alternatively if you place the additional scripts on the server in the WEB INF directory of your application where you will find your main R script located then because the actual working directories are always three subdirectories below the WEB INF directory the relative path to use in the source command will be source my_additional_R_script R This is what in effect the Upload Subsidiary files page see Section 9 11 of Rwui does for you automatically Similarly you may have a constant data source used by your R script each time it is run You could place this data on the server in the WEB INF directory of your application and access it in the R script using a relative path of my_ data_source Alternatively you could place the subsidiary R scripts and data sources in the library directory of your R installation A subsidiary R script would then be accessed in your main R script with the command source paste Library my_additional_R_script R sep Alternatively you could construct an R packag
6. You can then click through the pages of Rwui and edit the details on the relevant pages as required Please note the application description file does not contain the R script so you will need to upload this again on the Upload R script page The application description file also does not contain any subsidiary R scripts or reference data sets that you may have uploaded on the Upload Subsidiary files page see Section 9 11 and you will have to upload these files again The application description file is an xml file For the routine Rwui user an even simpler way to generate applications quickly is to create or modify this application description file directly in an editor Upload the description file check that the displayed Fascimile and Information Entered are correct and click through to the last page in order to create the application 9 2 Introductory Explanation Enter some text explaining to the user what your application does how to use it etc This is optional Any entered text will appear below the title of the application You can use html formatting tags in the text if you want Useful tags may be b b for creating bold text and br for putting in a line break The characters amp or anywhere in your text other than in html formatting tags might cause problems although this hasn t been the case in any of the browsers I ve tried If you need to use these characters in your text other tha
7. a aaa a a Pa eee a 8 13 O26 il ee cera Pe a he ee RE Re eS a ewe ee Daa ae ae 14 Of NAMIC reread he eee ee ee EM e RE Ree Re SE A eee ee 14 9 Resulta tile s 2 cc gab ed a SEES SDE LEG EERE Re Lea ORE aE BS 14 9 8 1 Displaying a results Ble s 6 20 2 bo ek bk be ee nw ee a A a 14 Oe 2 gt maps Map ne aiid ak nl aie Gh ee ha ae A 15 18 3 Geographic Goole Maps cay ada a Eee ee eS 16 9 8 4 Displaying results files of arbitrary name or unknown number 17 985 Laval of results Tes s ae ee whe eR ee ee a ee ee 18 9 8 6 Number of columns s sos e dow ale 5 ee oe Be ewe Ow a e H 19 9 8 7 Displaying current results on analysis page 1 2 ee ee 19 0 0 Process mIormation aose Gan Gao a EDS oe SRE ES aE Ee 2 ee Be we 19 9 10 Upload Bos ript a 2244442655 so be Ge bbe a eee be beeen ce ea ee 19 9 11 Upload sutsicary DES mona a Ke gra a ee eb Ge A he Bg Rey oboe A 20 9 12 Add an initial Login page ee 20 9 12 1 Providing Editing password s io cocoa a 21 9 13 Returning the results to the web page or by e mail o 21 0 13 1 E Mail Option Linux Oily iui lt 22 64458404526 eo ea se 21 0 14 Cancel Button Linux only e is ec ccc eda ee Ges ee AAA 22 9 15 Installing the application you have created e 23 10 Application description file 23 11 Modifiying the application 23 12 The completed application 24 a A o A A O 24 12 2 A moto about working directories Dieu a aa aa 24 12
8. amongst the input items available to you because you can put a radio button onto the page that has the same variable name as an existing radio button s For other input items if you enter a variable name that has already been associated with an input item on the page you get an error With a radio button you just get a warning message In this way you can split up a group of radio buttons on the page and put other input items and section headings between them This is useful if you wish for example to provide several alternative analysis methods each with their own set of parameters In which case radio buttons can be used to select the particular analysis method and input items for entering a method s parameters can be conveniently located below its respective radio button 9 4 8 File upload box A File upload box uploads a single file You can have any number of these on the web page How it works if for example you associate an R variable named my_data_file with a File upload box then the completed web application will assign the name of the file that the user uploads with this File upload box to the variable my_data_file eg if the user uploads a file called data txt then the application will automatically add the line my_data_file data txt to the beginning of the R script Please note that the application does not add a line to the script to actually read the file This means your R script needs
9. and the new results will appear as a second link at the bottom of the page and so on Clicking on a link brings up a Results page for the corresponding analysis The user can download individual results files from a Results web page by clicking on the name of the appropriate results file Alternatively each Results page also has a link which will download all the results files presented on the page and the html of the Results page itself In this way the user can view offline any saved Results web page plus its results files There are infact two links on the page one will download just the results files the other will also download any submitted data files that were used to produce the results If the results are displayed on a Google dynamic map then these two links will not be available The current results file s will also appear on the analysis page itself if this option was selected when the application was created 12 2 A note about working directories As mentioned above once the war file has been copied by you and unpacked by the server your application called for example myapp will have a directory under the Tomcat webapps directory called myapp Amongst other things this directory will contain a subdirectory called WEB INF Under this directory once the application has been used for the first time there will be a subdirectory called myapp store Each time the analyse button is pressed a unique directory with
10. geterrmessage error txt system nail command unlink unlnk command recursive TRUE q Then when the analysis has finished zip up the results files by pasting the following at the end of your R script before uploading it to Rwui this extracts the hexadecimal submission id pth lt unlist strsplit getwd id lt pth length pth 1 zip command lt paste zip id zip my_results_table txt my_results_graphs pdf sep system zip command Then e mail the zip file as an attachment by including the following code nail command lt paste nail s message_subject a paste id zip r from_address to_address lt message txt system nail command wait TRUE Then clear results files from server since the SessionListener is turned off with this line of code unlink results recursive TRUE 9 14 Cancel Button Linux only If the R script of your webapp can take a significant amount of time to run you may wish to include a Cancel button on the web page of your webapp In this way a user of the webapp can stop an unwanted R analysis that has been started in error Any files produced by the R script prior to cancellation are also deleted For a webapp in which the results are returned to the user by e mail the Cancel button will stop the last submission Any prior submissions that are still running won t be cancelled and cannot be cancelled by the Cancel
11. if a parent radio button or check box is not ticked then its child input items are ignored so won t cause validation problems if currently they are empty This will make things easier for users of your application For example in the Section 9 4 7 Radio Buttons we described how you may wish to provide several alternative analysis methods on the page each with their own set of parameters Radio buttons could be used to select a method with the input items for entering a method s parameters located below its 13 respective radio button In this case it will be easier for the user if they don t have to bother about the presence and validity of values in the parameter input items corresponding to the analysis methods that they have not currently selected This can be achieved by linking each parent radio button with its child input items 9 6 Linking On this page you set up the parent child linking of validation Possible Parent checkboxes and radio buttons with their options are named along the top of the table Potential Child input items whose validation could depend on them are named down the side Tick the boxes to link items An input item can be the child of more than one parent although for any given parent radio button an input item can only be the child of one of its options 9 7 Name Enter a short name for the application which will appear as the final part of the URL of the site eg If you ente
12. to include a line to read the file whose name is stored in the variable named my_data_file eg my_data scan file my_data_file The file data txt will have been automatically stored in the script s working directory so you don t need to include any path to the file 9 4 9 Multiple Replicate File upload page This page is for uploading an unspecified number of files When you select a Multiple Replicate File upload page as the input item first of all you enter the name of the R script variable associated with the multiple files and optionally add an explanation for the user 10 How it works if for example you associate an R variable named my_data_replicates with a Multi ple Replicate File upload page then the completed web application will assign the names of the files that the user uploads to my_data_replicates in the form of a list eg if the user uploads three files called replicatel txt replicate2 txt and replicate3 txt then the application will automatically add the line my_data_replicates c replicatel txt replicate2 txt replicate3 txt to the beginning of the R script As for the File upload box your R script needs to include line s to actually read the files whose names are stored in the variable that you have associated with the Multiple Replicate File upload page After entering the name of the R script variable associated with the multi
13. was created and a password was specified at the time then the text file passwords txt will contain the password one word and nothing else and editing the password is simply a matter of changing the word in this file If a password was not specified when the application was created then the password can be provided by inserting your chosen word for the password into this file If the individual username password pairs option was chosen then the username password pairs must be inserted into the file passwords txt with one username password pair per line and with each username and password separated by a comma An example would be jack red gold jill black iron tom brown copper dick green tin harry blue zinc So a username password file can be stored off the server and when changes are required conveniently edited in a spreadsheet then saved as a csv file called passwords txt and copied to your application s WEB INF directory on the server overwriting the existing passwords txt file 9 13 Returning the results to the web page or by e mail The web application can return the results online to the user s web browser Alternatively the results can be returned offline to the user via email in which case after submitting data for analysis the user can close the browser window if required Please note that the e mail option only works when the application is installed on a Linux machine It will not work w
14. 3 A note about paths subsidiary R scripts and constant data sources 25 12 4 A note about space on the server lt cc sc ee es ee ee 25 13 Tomcat Installation 26 ToL Windows path to TOMCA 4 2604 60004 a a ee a a ek ee ee eS 26 14 Web application servers other than Tomcat 26 15 R installation 27 15 1 Windows path to bin directory o 27 16 Error and Warning messages 27 17 Browser Navigation Buttons 28 18 FAQ Troubleshooting 28 19 Acknowledgments 29 20 Disclaimer 29 21 Any questions 29 1 Introduction Rwui is a web application that is used to create web applications for running R scripts All the code is generated automatically so that a fully functional web interface for an R script can be downloaded and up and running in a matter of minutes No extra scripting is required no new code needs to be learnt not even HTML it s all done for you A user friendly web interface for an R script means your script can be used by anyone even if they have no knowledge of R Since the web interface will run on a server the application can be accessed remotely and the user does not need to have R installed on their machine In addition updates to the R script need only be made to the one copy sitting on the server 2 Requirements In order to use the completed web applications created by Rwui you will need an installation of 1 A Java webserver such as Tomcat version 6 0 35 or later see details of Tomcat in
15. Creating user friendly web interfaces for R scripts automatically Richard Newton and Lorenz Wernisch August 15 2012 Contents 1 Introduction 3 2 Requirements 3 3 Quick tour 3 4 Demonstration Application 4 5 Technical Report and R News Article 4 6 Key features 4 OG Wey Tealures ol WU nos bes nes e a ee Be GA wn a eo ew SE ee Be de 4 6 2 Key features of applications created by Rwui 0 0 0000 eee eee 4 7 Installation of the download 5 8 R script requirements 6 9 User manual for Rwui 6 QU AES sc aaa Be Gee Dy Ge MG Ses ERE a ee ee Re 6 9 2 Introductory Explanation s 4 45284 2504 4 2 crasas ES 7 Oe Further Instrucciones oros e Wee ee ee a A we a 7 OA Input VariaDIES s kak ase Soe ee A a el BR ey Se A 7 941 How it Works sus gre acd ee eee eRe A BH ale Boe es 8 9 42 Input Variable amine 44 scs eses ee goh ee Dee eS 9 9 4 3 Delete Current Item 2 aa ee ek ee we ee ea Pa a eae e 9 O44 Section Heading eo s eoe weca aa Goa a ae ewe a ee Aaa e a Ae 9 0 45 Drop down list oe 2 4 4 5 6 daw be o a a Oe E A ad ae 9 9 46 Multiselect Ist cer e eaaa eok a i dp e e a a a aa e d oe a 9 947 Radio Buttons c s sor esaa aa ea 24 a ra phi a Rees a i e Shae ee 10 gS Pleuplad DO o e ari ans Diskda e dee We es Se he ee oe a RTE e ea ai 10 9 4 9 Multiple Replicate File upload page 10 9410 Zip file upload DOW 2 o e n doaa a eel we Be ea a 11 DA TE OAR Cutty DOR o oaos oe a RR ee A we eS 12 US Vahdat On xs as aa
16. Rwui_demol tgz or Rwui demol zip is also available for down load Some cel files cels tgz or cels zip for testing the demonstration application can be downloaded from here These cel files are from Choe S E Boutros M Michelson A M Church G M Halfon M S Prefered analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset Genome Biology 2005 6 R 16 1 15 5 Technical Report and R News Article Another source of information besides the User Manual see Section 9 is this Technical Report which gives a technical overview of Rwui The R News Article gives a general introductory description of Rwui 6 Key features 6 1 Key features of Rwui e Flexible you can backtrack edit and insert as you design your application e Whole range of input items available text boxes checkboxes file upload etc e Section headings can be included on the web page e Facility for uploading of an arbitrary number of files for example microarray replicates e Facility for grouping uploaded files for example into Diseased and Control microarray data files e A Login page can be included e Application details saved in application definition file for reuse and modification 6 2 Key features of applications created by Rwui e User input values checked for validity prior to processing Real time progress information displayed when running the application e Repeat analyses with different p
17. a 15 digit hexadecimal name is created in the directory myapp store Under this uniquely named directory is a subdirectory called results into which the R script writes any results files Once the R script has finished the web application looks in this directory for the files to display on the Results page The application also uploads any data for processing into this directory This means these data files will also appear in the list of results on the 24 Results page This gives the user the opportunity to check that the correct data has been submitted for processing and has been uploaded correctly When the application is created the R script has a line automatically added at the beginning to set the working directory correctly Important note So it is important that the R script you upload does not set the working directory at any point 12 3 A note about paths subsidiary R scripts and constant data sources Normally you will not have to bother about paths on the server Rwui will have arranged things so that everything is in the right place and your R script will not need any path information If your main R script requires subsidiary R scripts or data files these can be incorporated into the application using the Upload Subsidiary files page see Section 9 11 of Rwui which arranges the correct paths for these files automatically However situations might arise when you need to manually include path information in your
18. a password to be entered If one password for all is chosen then the password to be used can be specified on the next page of wui Alternatively you can leave this blank and provide a password by editing the application s password file once your application is installed on your server And you will be able to change the application s password at any time by editing the password file If the individual username password pairs option is chosen you will need to provide the username password pairs by editing the application s password file once your application is installed on your server If the individual username password pairs option is chosen in the finished web application when a user logs on the application makes their username available to the R script as an R variable called username which is automatically assigned in the R script right at the beginning of the code In this way the username can be used not only for control of access to the application but also for customising the R analysis for specific users 20 9 12 1 Providing Editing password s The password file is called passwords txt and can be found in the WEB INF subdirectory of your application once the application has been installed on your server see Section Installing the application you have created 9 15 below for an explanation about the WEB INF directory If one password for all was chosen when the application
19. arameters and data files new results added to list as a link to the corresponding results page e Results files displayed on results page and available for download e The user entered parameters and uploaded data files can also be checked on the corresponding results page e Created application is Java based and platform independent 7 Installation of the download What does the download contain Once uncompressed the download contains the complete application including all the source code in a number of directories All the files are included for the benefit of anyone who would like to make modifications of their own to the application for example changing the layout of the web pages Normally however no modifications are necessary in which case only one of the files within the download is required This is the war file in the deploy directory What do I do with the war file Rwui creates Java based web applications that use the Apache Struts framework so the completed applications will run on a Tomcat server http tomcat apache org Tomcat is very simple to install on both Unix and Windows machines details of Tomcat installation in Section 13 below All that needs to be done to use a web application created by Rwui is to place the completed application s war file in your Tomcat server s webapps directory Further details on what to do with the war file are given in Section Installing the application you have cre
20. ated 9 15 below Whilst Tomcat is the recommended web application server to run the applications created with Rwui the applications should run on many other Java web servers Please see Web application servers other than Tomcat in Section 14 below How can I make my new application website available to others You probably start with a local installation of Tomcat on a stand alone machine in which case web applications are accessed in a browser on the machine via the localhost 8080 URL see details in the section on Tomcat installation in13 below If the port you specify for Tomcat default 8080 is accessible from outside other people can access your application by substituting the IP address or machine name of your machine for localhost Note however that not all users are allowed communication via port 8080 If the website should be accessible to a wider community we recommend that you link Tomcat to a general webserver such as Apache see http tomcat apache org faq connectors html about connectors to Apache which under most installations of Apache allows the user to access your application via the standard web port 80 8 R script requirements An R script requires a few simple modifications in order to be run by an application created by Rwui 1 The input variables of the R script must be named according to the rules of both R and Java variable naming see Section 9 4 2 Input Variable Naming below But varia
21. bles in the R script other than the input variables do not need to conform to the rules of Java variable naming 2 The R script must not set the working directory 3 Any results to be made available to the user on the Results page must be written to files If the files are to be displayed on the Results page they must be suffixed with either txt or for images png or jpg If the files are just to be linked to or downloaded from the Results page then the suffix is irrelevant 4 Rwui offers the option of informing the user of the application continually about progress in the R script In this case the R script needs to periodically append lines to a file which must be called process_info txt with progress information for the user 9 User manual for Rwui Rwui takes you through a series of webpages in order to define and create your application The following steps need to be undertaken in sequence 9 1 Title Enter a title for the application which will appear in the banner at the top of each page Alternatively you can enter a previously saved application description file When you create an application the download will contain amongst other things an application description file more details about application description files in Section 10 below If you wish to modify an existing application instead of entering all the details again all the information can be automatically uploaded from the application description file
22. d into the R 11 script using the filenames held in the user s experimental structure file without problems arising from the varying and unknown directory structure that the user might have incorporated into their zip archive file 9 4 11 OAR entry box An Other Application Results OAR entry box allows you to link two or more applications that you have created using Rwui the results of one application serving as input to the second The set of analysis results produced by the first application to use as input to the second application are specified by their hexadecimal submission ID if the results are held on the server in an active session of the first application or their zip file name if the results have been saved to a local disk You can select whether you want the second application to access the results of the first application from just the server from just a local disk or more usefully from either the server or a local disk To include an OAR entry box in an application you will need to supply 1 The name of the other application whose results you want to use i e the last part of the URL see Section 9 7 eg my first_app 2 The name of the file of results that the other application produces and which you want your second application to access eg my_first_results txt 3 The name of the variable that the R script of the second application uses to hold the name of the other application s results
23. e 14 Web application servers other than Tomcat Tomcat is the recommended web application server to use to run the applications created with Rwui but the applications should in theory run on many other Java web servers We currently have not tried any other than Tomcat so if you do need to use another Java web server we would recommend thorough testing The applications have been created using the Apache Struts framework http struts apache org so should work with J2EE web application servers compatible with the Servlet API Specification ver sion 2 2 or later and the JavaServer Pages JSP Specification version 1 1 or later If you need to use another web server some useful information can be found in the Struts installation documen tation http www jajakarta org struts struts1 2 documentation ja target userGuide installation html The link will take you to a page towards the foot of which there is a section Installing Struts With Your Servlet Container that gives specific information about installing war files on a number of different web 26 application servers If you encounter problems with a particular application server it would be worth searching the struts user mail archive http www mail archive com user struts apache org Any feedback on using applications created with Rwui on web servers other than Tomcat would be most useful contact rm305 cam ac uk preferably with Rwui somewhere in the subject line 15 R insta
24. e out of all your R scripts and or data sources install the package in your R library and then access them in your main R script using the library or require commands In which case you will not have to bother about paths in your R script Details on how to create an R package can be found on the R website in the section Writing R Extensions 12 4 A note about space on the server Even if the data files have not been changed each time the analyse button is pressed they will be copied over to the new uniquely named submission directory If the user presses the Clear Page button then all their current submission directories and their contents are deleted on the server But if the user exits the application by closing the browser window without pressing the Clear Page button then the submission directories and their contents will remain on the server To stop the server from becoming clogged with data the completed web application includes a SessionListener The SessionListener detects 25 when a session is about to expire By default this occurs 30 minutes from when the application was last used but the session timeout can be changed in the Tomcat server configuration if necessary in the Default Session Configuration section of the file tomcat home conf web xml On detecting a session expiring the SessionListener removes the submission directories associated with the session 13 Tomcat Installation Installing Tomcat o
25. e to display the additional information in a new browser window you don t need to do this but you will be asked for the default size of the new browser window and its position on the screen The image map file eg map csv is a comma separated file of integers with the same number of rows and columns as the number of rows and columns in the image file eg image png Each integer entry in the image map file indicates which group the pixel in the same position in the image belongs to When the image is clicked the row and column of the clicked pixel is recorded These coordinates are used to find from the image map file which group the pixel belongs to The look up table lut csv is then used 15 to find which supplementary file corresponds to this group number And this supplementary file is then displayed for the user The look up table file simply contains two comma separated columns the group number is in the first column and the name of the group s supplementary file is in the second column If the map file contains an integer entry i e group number that doesn t appear in the first column of the lookup table then the application will display a blank file So areas of the image which don t need to be clickable can be given a group number eg 0 in the map file then if the lookup table doesn t contain an entry for this group number these areas won t generate a supplementary file when clicked A simple demonstration applicat
26. f items from the list After entering the R variable name and any explanatory text you will be taken to a second web page where you need to specify whether the associated R variable is numeric or text and then a third web page where you enter the possible values that the variable can take If the associated R variable is numeric then only numeric values or NA can be entered as possible values that the variable can take If for example an R variable called my_list is associated with a text Multi select list and the items in the list are all colours and in the completed application the user selects the items from the list red yellow and green then the following line of code will automatically added to the beginning of the R script before it is run my_list c red yellow green V If the Multi select list is numeric then a similar line of code is added but without the quotation marks eg my_list c 0 143 5 21 1 976 9 4 7 Radio Buttons Similarly for Radio Buttons after entering the R variable name and any explanatory text you will be taken to a second web page where you need to specify whether the associated R variable is numeric or text and then a third web page where you enter the possible values that the variable can take If the associated R variable is numeric then only numeric values or NA can be entered as possible values that the variable can take Radio Buttons are unique
27. file eg file_from_first_app How it works if you add an OAR entry box to an application eg called my_second_app with the above example entries my_first_app my first_results txt file_from_first_app then each time this second application is run a new line is automatically added to the beginning of its R script The content of this line will depend on whether the user is entering results currently held on the server from an active session of my_first_app or is entering results from my_first_app which they have previously saved to a local disk From the server The user enters in the OAR entry box the hexadecimal submission ID eg 2ED41AB9FCC357FA corresponding to the results from my_first_app that they wish to use Then the line automatically added to the beginning of the R script of my_second_app will be file_from_first_app tomcat home my _first_app WEB INF my first_app_store 2ED41A B9FCC357FA results my first_results txt Note that no line is added to the R script to actually read the file The R script that you upload when creating my_second_app must contain a line to read the file whose name and path is held in the R script variable file_from_first_app eg your script should include a line such as data_from_first_app read table file file_from_first_app From a local disk The user enters in the OAR entry box of my_second_app the results file p
28. from a file containing a list of the names of results files will be displayed the same size the width and height being specified on this page 9 8 5 Layout of results files The layout of the results files to be displayed is controlled by layout tables You need to assign each results file to be displayed to a table Files which are lists of results files must be assigned a table number on their own one table per file Files which are actual results files can be combined within a table Tables will appear down the page in ascending order of table number Within a table for files which are lists of results files the results files will be displayed on the page in the order in which they appear in the file containing a list of the names of results files i e if the table is divided into columns filling a row left to right before starting a new row So you can arrange results files in a logical way on the page by specifying the order in which they are written to the file containing a list of the names of results files For files which are actual results files which have been assigned to the same table the order they appear will be determined by the order in which their names were entered on the Enter the name of a results file to be displayed page 18 9 8 6 Number of columns On the next page of Rwui you can specify how many columns to divide each table into If more than one results file is to be displayed in a table and yo
29. h each results file is displayed can be specified here Files which are to be displayed in this way must end in either txt or for images png or jpg Note that Internet Explorer won t display png s so jpg s will be necessary if your completed application might be accessed via IE 14 9 8 2 Image Map Giving an image an image map makes the image clickable with the outcome of clicking depending on where on the image the mouse was clicked So it allows the user to see displayed extra information about an area of an image when they click on that part of an image An image can be given an image map on the page Enter the name of a results file to be displayed Images contained in lists entered on the page Enter the name of a list of results files currently cannot be given image maps The image map facility will only work when the results are displayed on the web page not when they are e mailed to the user because an image map produced by Rwui is a server side image map i e it needs the server the web application is installed on in order to work 1 The image i e a png or jpg file eg image png 2 The lookup table which tells the application what information to display when a particular part of the image map is clicked This is a csv file eg lut csv 3 The map of the image which relates the image to the lookup table This is also a csv file eg map csv See below for further information about these files T
30. he R script needs to write these files to its current working directory eg write csv image_map file map csv The R script also of course needs to actually produce all the information to be displayed when a particular part of the image map is clicked These files can be images png or jpg or text txt The R script needs to write these files to a subdirectory of the current working directory called mapinfo eg write area_1_info file mapinfo area_1_info txt The subdirectory mapinfo is created automatically When the user clicks on the image displayed in the results section of your web application the information associated with that part of the image will be displayed for the user You can choose to have that information displayed on the same page as the clickable image or have it displayed in a new browser window there will be a new browser window to display this information for each set of results i e for each submission If you chose to display the additional information on the same page as the image you need to tell Rwui to display this information and whereabouts on the page to display it and what size to display it To do this simply enter the name of the lookup table file eg lut csv as a results file to be displayed on the page Enter the name of a results file to be displayed This will reserve a space on the page to display the additional information at the correct size If you chos
31. hen installed on a Windows server 9 13 1 E Mail Option Linux only If the E Mail option is selected the web application must contain a text entry box associated with a variable called email_address If this input item is not present Rwui won t allow this option to be selected and you will need to click back and add it to the page With the E mail option selected Rwui creates a web application that will set the R script running but not wait for it to finish It will return a message to the web page immediately informing the user that the analysis has started and the results will be e mailed to the address they entered on the page The user can then close the browser window if required or submit further jobs No process information or graphical process information is displayed Note that the SessionListener is also turned off so files will not be deleted from the server automatically 21 Your R script must contain code for e mailing the results of the analysis Here is some example R code for a Linux system using the mailing program nail Firstly arrange for any error messages to be e mailed to the user if the analysis fails and for any results files to be deleted by pasting something like this at the beginning of your R script before uploading it to Rwui unlnk command lt results nail command lt paste nail s message_subject r from_address to_address lt error txt options error quote write
32. hen the webapp will display the map that is featured as the Quick example in the Google static maps guide We have published a paper on displaying Google static maps Creating web applications for spatial epidemiological ana Dynamic Map To include a dynamic geographic map in the webapp you are creating check the box asking whether the file to display is a dynamic geographic map For a dynamic map your R script will need to write a file containing the javascript for creating the map You enter the name of the file that will contain the javascript as the name of the results file to be displayed Keep the name simple eg dynmap js Currently you can have only one dynamic map displayed on a page Here is a simple example of the type of file the R script must write function initialize var latlng new google maps LatLng 34 397 150 644 var myOptions 1 zoom 8 center lating mapTypeld google maps MapTypeId ROADMAP var map new google maps Map document getElementById map_canvas myOptions The term map_canvas in the above must not be changed to anything different but apart from that any changes additions can be made that conform to the Google dynamic maps API Further details on how to display dynamic Google maps in applications created by Rwui are given in the document Documentation on displaying results on Google dynamic map with examples step by step guides and helper functions To include a clickable dy
33. identifier related to the name of its corresponding data file These type of results files can be displayed by applications created by Rwui Specify a filename eg my_list_of_results_files txt and select the option Name of a file produced by the R script containing a list of the names of results files produced by the R script In the R script as well as writing results to files the names of these results files need to be written to the file my_list_of_results_files txt For example if the R script contains the lines write my_data_1 file results_1 txt and write my_data_2 file results_2 txt then to have these two results files displayed the R script also needs to include the lines write results_1 txt file my_list_of_results_files txt append TRUE and write results_2 txt file my_list_of_results_files txt append TRUE The name of each results file must appear on a new line in the file my_list_of_results_files txt The results file names themselves still need to end in txt png or jpg in order to be displayed All three types can appear in the list Any number of files containing a list of the names of results files can be specified in an application And the same application can also display other results files in the more direct way i e where the name of the results file is specified explicitly when creating the application All the files displayed
34. ing an unspecified number of files 5 Drop down list list of possible values numeric or text for an R variable in a drop down list 6 Multi select list list of possible values numeric or text for an R variable which can be a list of values 7 Radio buttons list of possible values numeric or text for an R variable in a column of radio buttons 8 Checkbox for assigning R variable as being TRUE checkbox ticked or FALSE checkbox unticked 9 OAR entry box Other Application Results entry box for entering the results from another appli cation created by Rwui 10 Zip file upload box box for uploading a zip file which will be automatically unzipped 11 Text area input box text box with several rows used for example to allow users to add notes about each submission 12 Section Heading not actually an input item included here for convenience see Section 9 4 4 Section Heading below 13 DELETE CURRENT ITEM also not an input item included here for convenience see Sec tion 9 4 3 Delete Current Item below There needs to be one input item corresponding to each of the input variables of your R script that is those variables in the R script that require a value supplied by the user By default new input items are added to the page in order i e below the previous input item If you would like to insert an input item between existing input items then change the number in the box Current i
35. ion can be tried out here Image Map Test application This simple test application can be downloaded here image_map test tgz The war file could be installed in order to test that the image map function is working correctly on a Tomcat server The R code from the test application is linked to here image_map _test R this generates a simple image image png a corresponding map file map csv a lookup table file lut csv and four supplementary infomation files to be displayed when the image is clicked The R functions grconvertX x from user to device and grconvert Y y from user to device can be very useful when creating map files These convert plot coordinates user coordinates into device pixel coordinates which will correspond to row and column values in the map file An R function that takes user coordinates of rectangles ellipses and lines and creates a map file can be found here createlmageMap R 9 8 3 Geographic Google Map A web application created by Rwui can also display the results of the R analysis as a geographic map A typical application would have the user of such a webapp uploading a data file to your server The data is then analysed by your R script on the server The R script produces a text file of results These results are then displayed for the user on a geographic map The geographic map may be either a static Google map s or a dynamic Google map In addition there is the
36. llation Just the normal R installation is required 15 1 Windows path to bin directory If using Windows remember to set the path to R s bin directory something you may not normally think to do To set the path go to Start Control Panel System Advanced Environment Variables In the System Variables box scroll down and select variable Path and press Edit Add the path to R s bin directory eg by adding something like C Program Files R R 2 1 0 bin to the separated list Then reboot the PC for the change to take effect As of R version 2 15 the path that needs to be specified has changed to C Program Files R R 2 15 1 bin x64 for 64 bit machines and C Program Files R R 2 15 1 bin i386 for 32 bit machines If in doubt find the path on your machine to the file Rterm exe 16 Error and Warning messages If an R error occurs when your web application is being used it will be displayed on the web page To track down the cause of the error look at the actual R script that is being run completeRscript R which can be found in the directory tomcat home webapps myapp myapp store hexradecimal_submission_id if you called your application myapp The R error is displayed on the web page because the R options command is automatically set by the application at the beginning of the R script so that if an error occurs the error message is written to a text file called
37. n both Unix and Windows machines is very simple and straightforward For instruc tions on downloading and installing Tomcat click here tomcat_installation html If you don t wish to provide remote access to your application then Tomcat can be installed for users on a stand alone machine You may also wish to install Tomcat on a stand alone machine so that you can test the applications you have created before they are put on a deployment server When installed on a stand alone machine web applications are accessed in a browser on the machine via the localhost URL eg http localhost 8080 myapp Note that the portnumber being used for Tomcat localhost is usually 8080 but if necessary the portnum ber in use on your system can be found or changed in the file server xml which will be located in the tomcat home conf directory look for the section Define the Tomcat Stand Alone Service 13 1 Windows path to Tomcat An important point to note when installing Tomcat on a Windows machine when the installer asks into which directory Tomcat should be installed don t install into the default directory install into a directory called for example C tomcat tomcat 5 5 The reason for this is that the default choice will have spaces in the path which will prevent applications from running Dots in the directory names also causes problems as might other characters so just use alphanumerics and hyphens as shown in the exampl
38. n in html formatting tags and want to be quite safe then use their html symbols amp amp amp gt amp lt and amp quot 9 3 Further Instructions If you need to provide the user with more instructions or background information than there is room for on the web page you can upload a file of instructions and a link to this file will be automatically added to the web page of your application Choices of file format are Word doc PDF pdf or HTML html Please note if using an Application Description File see Section 10 ADF to load a previously created application back into Rwui for editing the file of instructions will have to be reloaded it is not included in the ADF The HTML format may be the most convenient for your users in that clicking the link on your application will open a new window displaying the instructions whilst the browser may need to download Word or PDF documents before they can be viewed Creating HTML formatted text is simple since editors like Word and OpenOffice can save documents as html and latex documents can be converted using the latex2html program 9 4 Input variables On this page you create the input items that will appear on your application s web page 1 Numeric box for entering the value of an R numeric variable Text box for entering the value of an R text variable File upload box box for uploading a single file 2 3 4 Multiple Replicate File upload page page for upload
39. namic geographic map in the webapp you are creating check the appropriate box The steps then required are similar to those required for an ordinary dynamic geographic map and full details are given in Documentation on displaying results on Google dynamic map 9 8 4 Displaying results files of arbitrary name or unknown number Often the name of the results files produced by an R script will be constant In applications created by Rwui because the results from an analysis are uniquely identified by the directory in which they are saved there is no need for the R script to add a unique identifier to the results file that depends 17 for example on the name of the data file the user has uploaded Calling results files results txt or results png is sufficient However in some circumstances the R script will need to add a unique identifier to the results files which will be unknown prior to runtime Also in some circumstances the exact number of results files that the R script produces will be unknown and variable For example if the user of an application created by wui uploads a number of data files using a Multiple Replicate File upload page or a Zip file entry box and the R script produces a results file for each of these data files The number of results files will vary depending on how many data files the user has uploaded The exact names of the results files will also vary since the R script will be naming each results file with an
40. nput position The position numbers of existing input items are given on the right hand side of the facsimile page If a Multiple Replicate File upload page is included this will always be at position 1 Select the appropriate type of input item for one of the input variables in your R script then on the next web page type in the name that the variable has in your R script exact same spelling and case Next enter some text explaining to the user what they should enter using this input item optional Again html formatting tags may be used The explanatory text you enter here will appear alongside the input item on your application s web page Repeat for all the input variables of your R script A facsimile of the web page you are creating will appear at the bottom of the page When all input items have been added correctly press Finished composing page 9 4 1 How it works If for example you associate the R script variable my_num with a Numeric entry box Then the completed application will automatically add a line to the beginning of the R script that assigns whatever value the user enters in this Numeric entry box on the web page to the R variable my_num For example if the user of the completed application enters 1 234 in the Numeric entry box then the line my_num 1 234 will be automatically added to the beginning of the R script before the script is run Similarly for a Text entry box if for example you a
41. nput variable then enter my_input_variable as the input variable name when creating the web application with Rwui and add the line my input variable my_input_variable at the beginning of your R script The names of variables in the R script that are not input variables do not need to conform to the rules of Java variable naming 9 4 3 Delete Current Item Select this from the list if you need to remove an input item already added to the page Specify the input item to delete using the Current input position box the position numbers of input items are given on the right hand side of the facsimile page Then press Enter 9 4 4 Section Heading If the web page contains many input items you may wish to divide them up into sections The selection Section Heading allows you to insert a sub heading on the web page and or some explanatory text positioned below the heading 9 4 5 Drop down list For a Drop down list after entering the R variable name and any explanatory text you will be taken to a second web page where you need to specify whether the associated R variable is numeric or text and then a third web page where you enter the possible values that the variable can take If the associated R variable is numeric then only numeric values or NA can be entered as possible values that the variable can take 9 4 6 Maulti select list A Multi select list is similar to a Drop down list but allows the user to select a number o
42. option of making a dynamic map clickable That is users of the webapp can define regions of interest by clicking on the map with the mouse When the Analyse button is pressed the coordinates of the region of interest are automatically made available to the R script Regions of interest may be either circles irregular polygons squares or rectangles all of which are dynamically resizable and draggable Static Map To include a static geographic map in the webapp you are creating check the box asking whether the file to display is a static geographic map and enter the name of the text file of results that the R script will produce Keep the name simple eg geomap txt or if the page has more than one map geomapl txt geomap2 txt etc The format of the results file produced by the R script is important Each line of the results file must contain the name of one valid static Google maps parameter followed by the value for that parameter Valid parameters are documented in the Google static maps guide The parameter name and the parameter value must be separated by an equals sign An example results file would be center Brooklyn Bridge New York NY 16 zoom 14 size 512x512 maptype roadmap markers color bluel label S 40 702147 74 015794 markers color green label G 40 711614 74 012318 markers color red color red label C 40 718217 73 998284 sensor false If the R script produced a results file containing the above information t
43. ple files you can choose whether to include a text box on the Multiple Replicate File upload page for specifying the group each file belongs to For example if the multiple files are microarray data then the data files may belong to either a Control group or a Diseased group How it works if you include this text box on the page then the completed application will automatically add a line to the beginning of the R script which assigns the group names that the user enters in this box to a variable named groups in the form of a list eg if the user entered Control when entering replicatel txt and Diseased when entering replicate2 txt and Diseased when entering replicate3 txt then the application will automatically add the line groups c Control Diseased Diseased to the beginning of the R script 9 4 10 Zip file upload box Uploading a large number of files using a Multiple Replicate upload page might be quite tedious An alternative is to zip all the files and upload them as a single file using a Zip file upload box Once uploaded the zip file is automatically unzipped into the current working directory where the files will be accessible to the R script A line is automatically added to the beginning of the R script that assigns as a list the names of all the files in the zip archive to the R variable you associated with the Zip file upload box when creating the applica
44. r myapp here then the URL will be http localhost 8080 myapp Hence the name you choose should not contain any spaces Permitted characters are all the alphanumerics and and _ 9 8 Results files The completed web application accesses the results produced by the R script by reading saved files So for the user to see the results your R script must write any results to files For example you should include lines like write table my results file my_results txt in your R script Any number of results files can be produced Once the R script has terminated the application looks at what files have been produced by the R script and lists them on the Results web page as links which the user can click on to view and or download If the R script writes temporary files these will also appear in the list of links on the Results page so they should be removed by the script using file remove 9 8 1 Displaying a results file You may however want to display the contents of some or all of the results files on the Results page straight away to save the user the trouble of having to click on a link To do this enter the name of the results files that you wish to be displayed one at a time If more than one results file is to be displayed on the Results page they will be displayed in order down the page or across the page see next paragraph in the same order in which their names are entered into wui The size of the box in whic
45. roduced by my first_app which they have previously saved to their local disk eg my first_app C7BA92D55FAF3B1 zip The file my_first_app C7BA92D55FAF3B1 zip will be uploaded to the current working directory of 12 my_second_app and unzipped there This creates a directory named C7BA92D55FAF3B1 contain ing the results files from my first_app including my_first_results txt And the line automatically added to the beginning of the R script of my_second_app will be file_from_first_app C7BA92D55FAF3B1 my_first_results txt Note that no line is added to the R script to actually read the file The R script that you upload when creating my_second_app must contain a line to read the file whose name and path is held in the Rscript variable file_from_first_app eg your script should include a line such as data_from_first_app read table file file_from_first_app If you need to enter more than one results file from the first application into the second application you can have the first application create an RData file of the required files and then enter this RData file into the second application For example in the R script of the first application save list c results_1 results_2 file my_first_app RData When creating my_second_app you would enter my_first_app RData as the the name of the file of results that my_first_app produces and which
46. ssociate the R script variable my_text with a Text entry box and the user of the completed application enters The cat sat on the mat in this box then the line my_text The cat sat on the mat will be automatically added to the beginning of the R script Drop down List Radio Buttons and Checkbox work in a similar fashion except the choices available to the user have been pre defined by you when creating the application For how File upload box and Multiple Replicate File upload page work see Section 9 4 8 File upload box and Section 9 4 9 Multiple Replicate File upload page below 9 4 2 Input Variable naming Important Note The names for the input variables of your R script must also be named according to the rules of Java variable naming i e permitted characters are any letter of the alphabet numbers and underscore To conform to both Java and R the variable names must start with a letter of the alphabet And this needs to be lower case Note that if the second character in the variable name is a letter then 1t must also be lower case But upper case letters are permitted elsewhere in the variable name So the character for example is not allowed If an existing script does use the character in the name of an input variable either replace the throughout the script with an underscore or reassign the variable at the beginning of the script eg if the script requires my input variable as an i
47. stallation in Section 13 or Web application servers other than Tomcat in Section 14 below 2 Java version 1 6 0_31 3 R a version compatible with your R script s see details of R installation in Section 15 below This would not normally be necessary but if you did want to make changes to the source code of the downloaded application you may want to consider Ant http ant apache org for rebuilding the application with the included Ant script Whilst the application was developed under Unix we have tested the web applications created with Rwui under Windows XP as well where they worked without modification 3 Quick tour A Quick Tour shows you how to use Rwui to create a website that uploads and analyses a table and eraphically displays the results More detailed instructions see Section 9 for using Rwui are given below To summarise using Rwui simply involves e entering details about your R script on a sequence of web pages e Rwui then generates the web application e which you can download either as a zip or tgz file e Either of these downloads extracts into a folder containing all source script and executable files of the application in particular a war file e Once the war is copied to the Tomcat webapps directory the application is ready 4 Demonstration Application We have prepared a more substantial demonstration application for analysing microarray data created using Rwui The complete application
48. t If you still proceed with the request you will end up at an error page and will have to restart your session from Rwui s start up page having lost all your work The above applies to the applications created by Rwui so you may wish to include a warning not to use the browser navigation buttons in the introductory text of the application you are creating 18 FAQ Troubleshooting 1 If the application produces no results files and it is installed on a Windows machine please first check points 13 1 and 15 1 above 2 If the application produces an error message An error occurred creating a directory and Tomcat is installed on Ubuntu it might be because Tomcat was installed by using the package manager which results in permissions problems The solution is to uninstall Tomcat with the package manager and re install it by simply copying the Tomcat tgz from the Tomcat website and installing it by unpacking the tgz in a convenient location on your machine See tomcat_installation html 3 The R graphics devices png and jpeg in an R script being run by an Rwui webapp may or may not work depending on how R was installed A more reliable graphics device in this instance is bitmap although you do need to have ghostscript installed on your machine Here is an example producing a png using bitmap bitmap file box png type png256 width 12 height 5 res 100 pointsize 8 boxplot dt dev2bitmap file box png type png256 width 12
49. t from Start gt Control Panel gt Administrative Tools Services 23 6 On Unix systems remember to cd to tomcat home webapps myapp and chmod a x srcmd sh 12 The completed application 12 1 Description If a Multiple Replicate File upload page has not been included then the completed application for running your R script consists of one web page where values of variables may be entered data uploaded if necessary and the whole lot analysed If a Multiple Replicate File upload page is included the completed application has two input web pages The user uploads the multiple files one at a time using a File upload box on the first web page Once completed a button takes the user to a second web page where values for all other variables and singleton data files are entered The application checks the validity of the values that the user enters and returns an error message to the page if values entered are not valid Only numeric values or NA can be entered into Numeric entry boxes Numeric Text and File Upload boxes cannot be left blank Multiple Replicate Files must be unique that is the same file cannot be entered more than once Text entered into Text boxes is trimmed of any leading or trailing whitespace that may inadvertently been entered Once analysed a link to the Results page appears at the bottom of the web page The user can change any of the variables and or data and re analyse
50. tion For example if you associated the R variable named zipfilenames with the Zip file upload box when creating your application and the user uploads a zip file containing three files replicatel txt replicate2 txt and replicate3 txt then the application will automatically add the line zipfilenames c replicatel txt replicate2 txt replicate3 txt to the beginning of the R script before it is run Please note that the application does not add a line to the script to actually read any of the files the R script you upload needs to do this Using a Multiple Replicate File upload page allows a group identifier to be assigned to each file If a Zip file upload box is used instead and group identifiers are required then a simple File upload box should also be included on the page by means of which the user can upload a file containing a table giving the structure of the experiment for example a table containing a column of filenames and a column of their group identifiers Using the filenames held in the experimental structure file is another convenient way of reading the data files into the R script If the user accidentally uploads a zip archive file which has some directory structure then this directory structure is not maintained when the zip file is unpacked on the server The data files are put into the top level of the working directory for the particular submission Hence they can still be rea
51. top level of the directory myapp created when you uncompressed myapp tgz or myapp zip eg download directory myapp myapp xml Our thanks to the developers of the Java package XStream http xstream codehaus org which has been used to create the xml file The XStream License can be viewed here xstream_license txt 11 Modifiying the application You may want to modify the application for example editing the jsp s to change the layout of the input and or the results pages If you want to modify the completed application then the download includes all the files necessary After you have modified the java or jsp files the application needs to be rebuilt and redeployed To do this using the included Ant script 1 cd to the directory download directory myapp or whatever you called your application 2 Edit the file download directory myapp build properties to add the path to the Tomcat directory on your system the path to the top level of Tomcat not webapps i e in Unix you will need a line like tomcat home or in Windows you will need a line like tomcat home C 3 In directory download directory myapp type ant clean all 4 Then type ant deploy The application will be rebuilt and the war file copied to your Tomcat webapps directory 5 Restart the Tomcat server Unix tomcat home bin startup sh Windows tomcat home bin startup bat or start i
52. u would like them displayed side by side rather than one below the other then divide the table into columns 9 8 7 Displaying current results on analysis page In applications created by Rwui the results of each analysis are accessed from a list of links at the foot of the analysis page But you also have the option of displaying the results files from the current analysis on the analysis page itself 9 9 Process information If your R script takes some time to execute you may want to provide the user with process information in order to inform them of the progress the R script is making If you would like to do this check the box For this facility to work your R script needs to periodically append lines to a file called process_info txt with progress information for the user i e you need to add lines such as write Starting the analysis file process_info txt append TRUE at strategic points in your R script The R function capture output can also be useful for appending lines to the file process_info txt For example from microarray analysis capture output expr rma data append TRUE file process_info txt The completed web application reads the file process_info txt every few seconds and displays it in a Javascript popup window So a user of your application needs to have Javascript enabled in their browser for this feature to work To enable Javascript In Mozilla go to Edit
53. which you have uploaded on the previous page with the line source file subsid_script Similarly if you upload a data file reference_data RData and provide the R variable name reference_data then you could access this data in the main R script with the line load file reference_data How it works The file for example my_subsidiary_script R with variable name subsid_script is uploaded and incorporated into the WEB INF directory of the application you have created The actual working directory for the main R script for each submission is always three directory levels below the WEB INF directory so the line subsid_script my subsidiary_script R is automatically added to the beginning of the main R script Please note if using an Application Description File see Section 10 to load a previously created appli cation back into Rwui for editing the subsidiary files will have to be reloaded they are not included in the ADF Further information on ways of including subsidiary files is given below in A note about paths subsidiary R scripts and constant data sources see Section 12 3 9 12 Add an initial Login page You may want to password protect your application by adding an initial Login page Two types of Login page are available One Login page requires only a password to be entered and all users use the same password The other type of Login page requires both a username and
54. ynchroAction and to Sterling Udell and John Coryat for the javascript file for map overlays ProjectedOverlay js Wolfgang Pichler for drawing draggable and resizable polygon javascript functions and Luke Mahe for drawing draggable and resizable circle javascript functions 20 Disclaimer The web applications created by Rwui come with absolutely no warranty Whilst every effort has been made to ensure Rwui will produce a bug free web application that will run your R script faithfully and correctly under all circumstances we cannot guarantee this and advise you to test thoroughly the completed application 21 Any questions We will be happy to answer any questions and would welcome feedback Please contact rn3050cam ac uk Preferably including Rwui somewhere in the subject line 29
55. you want my_second_app to access And the R script that is uploaded would now need to include a line such as load file file_from_first_app In applications created by Rwui users have two options when saving the results of an analysis either saving Results only or saving results plus the data files they have uploaded If the first application uses large data files it would clearly be best if users saved Results only to a local disk to use as input to the second application so that the data files from the first application are not unnecessarily uploaded to the second application 9 5 Validation Normally your completed web application checks the validity of the values that the user enters and returns an error message to the page if values entered are not valid Only numeric values or NA can be entered into Numeric entry boxes Numeric Text and File Upload boxes cannot be left blank You can turn off validation here but it is not a good idea to do this unless absolutely necessary Multiple Replicate file upload validation is not turned off and neither is the validation of OAR entry boxes If there are radio buttons or check boxes in the web application you also have the option to select linked validation of input items in your completed web application and the next web page will allow you to set this up You can link child input items with parent radio buttons and or checkboxes so that in the completed web application
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