CanReg5 Webinar 3: Migration fromCanReg4
Morten Ervik
International Agency for Research on Cancer,Lyon, France
Lyon, France, 31 May 2012
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Exporing the data
1. In CanReg4: “Analysis” -> “Export data”I Tick “Export all variables”.I Choose short variables namesI Under “Export File options” choose “Comma separated
variables”I Untick both “Format date” and “Correct Unknown”I Click “write data to file” and pick a file name that you can
find back easily in CanReg5. For example on the desktop.Click “save”.
2. Take a note of the number of records. (This should latermatch the number of Tumour records in your CanReg5system.)
3. Take a look at the data you have now exported and closeCanReg4.
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Exporting the dictionary
1. In CanReg4 go to “Data Entry” -> “Dictionary”2. Click “Export dictionary to text file”
That’s it
That’s all we need to do in CanReg4.
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Convert System Definitions
I Each registry can collect the variables they want, so weneed to migrate the definitions file from CanReg4.
I This is done using the “Tools”->”Convert CanReg4 SystemDefinition” tool in CanReg5.
I Since we go from a single table database in CanReg4 to arelational database in CanReg5, you’ll need to map thevarious variables to either Patient, Tumour or Source duringthis migration process.
I If you want to do some changes to your database - now isa good time.
I Refer to the previous Webinar, or the CanReg5 handbookfor more information.
I Note that some changes, length of variables etc, mightrequire editing of the data from CanReg4 before importingto CanReg5.
Log on to your new CanReg5 system
I Launch the CanReg server so that the database is builtand the system is ready to be logged in to.
I Log in with username “morten” and password “ervik”. (Youshould of course change this after first login.)
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Import the dictionaries
I Go to “File” -> “Data Entry” -> ”Edit Dictionary” inCanReg5.
I Import complete dictionary from fileI Pick the CanReg4 dictionary we exported earlier as
CR4<code>-D.TXT in your CanReg4 work folder.I Important: tick CanReg4 format.I Note that CanReg5 does not allow duplicate codes within
any dictionary, whereas CanReg4 did, so you might getsome errors stating that certain dictionaries were notsuccessfully imported due to that.
I Take a backup of your system.
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Import data
I “File”->”Data Entry”->”Import Data”I Click “Yes” to the question “Do you have all your data in one
file?”
I Choose the file containing the data we exported fromCanReg4.
I Preview it to see that it looks OK.
I Associate variables.I CanReg tries to “guess” where to store each variable, but
verify to be sure.
I Go to “Import File”I Leave “Data from previous CanReg version” ticked.I Click Import - and wait.
After data import
I Verify number of tumours in the database to make sure allcases have been migrated.
I Browse the data to see if you see anything suspicious.I If you do, confirm the existence also in CanReg4.
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Import population data sets
I For each population data set you want to migrate:I Click “Tools”->”Load CanReg4 Population Data Set”.I Load PDS files from the CanReg4 installation. (Located in
the CR4-SYST folder.)I Verify them.
I Are the filters are correctly written?I Does the pyramids look OK?
I Save them to the database.
Outline
Getting everything out of CanReg4Exporting the dataExporting the dictionary
Getting everything into CanReg5Convert System definitionsImport the dictionariesImport dataImport population data setsFinishing touches
Live Demo
Summary
Finishing touches
I Add users, remove/change the default “morten” user.I Take another backup.
Live Demo
Summary
I Export the data and dictionary from CanReg4I Convert (and potentially edit) system definitions in
CanReg5I Import dictionariesI Import dataI Import population data setsI Add users
Summary
I Export the data and dictionary from CanReg4I Convert (and potentially edit) system definitions in
CanReg5I Import dictionariesI Import dataI Import population data setsI Add users
Summary
I Export the data and dictionary from CanReg4I Convert (and potentially edit) system definitions in
CanReg5I Import dictionariesI Import dataI Import population data setsI Add users
Summary
I Export the data and dictionary from CanReg4I Convert (and potentially edit) system definitions in
CanReg5I Import dictionariesI Import dataI Import population data setsI Add users
Summary
I Export the data and dictionary from CanReg4I Convert (and potentially edit) system definitions in
CanReg5I Import dictionariesI Import dataI Import population data setsI Add users
Summary
I Export the data and dictionary from CanReg4I Convert (and potentially edit) system definitions in
CanReg5I Import dictionariesI Import dataI Import population data setsI Add users
Summary (contd.)
I The migration proc this is detailed, step by step, inAppendix C of the CanReg5 handbook, available at:http://www.iacr.com.fr/CanReg5/CanReg5-instructions.pdf(Or from within CanReg5 itself.)
Future webinars
I Next webinar will take place the 4th of September, at14h00.
I Theme:I Data Entry
I Quality controlI Patient deduplicationI Using browse/filter to find cases
I Future themes:I AnalysisI Import of data
I Slides and videos will be put online at the GICR website;http://gicr.iarc.fr
For Further Information I
Ervik, MortenCanReg5 - the handbook2009-2012Available online at the IACR web page under software
CanReg5 web pagehttp://www.iacr.com.fr/canreg5.htm
@canreg twitter feedhttp://twitter.com/canreg