canreg5 webinar 3: migration from canreg4

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