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RTDS VISIR Helpdoc - canceruknet Home

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RTDS VISIR Helpdoc - canceruknet Home ...

User instructions for the Visir v3 / Oncentra Tool 10/09/2009

    User instructions for the Visir and Oncentra Toolkit to extract

    the National Radiotherapy Dataset (RTDS v3.7)

1. Installation

    The package RTDS_Toolkit_VISIR_v2.0.5.execan be downloaded from the RTDS

    website www.canceruk.net/rtservices/rtds/visir_Oncentra/index.asp. It contains all the files you need to create the toolkit on your PC. Select a suitable location for the

    download then locate the file and double click this executable file to install the set up files

    in a folder of your choosing. You no longer have to choose the default install directory!

Open the folder you chose and double click the file „Setup.exe‟. This runs the installation

    wizard. The following screens will appear. Please select „Next‟ on the first 4 screens and „Close‟ on the fifth and final screen.

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    User instructions for the Visir v3 / Oncentra Tool 10/09/2009

The location you select in the above screen will herein after be referred to as the

    „Installation Folder‟ and it (and its sub-folders) will contain all the files you need. The default installation location is now in your Program Files, within a folder called

    NatCanSAT. You may place the executable and supporting files wherever is appropriate

    on you PC although it must be able to see the location where you will ultimately store

    your database files either directly or via a mapped drive. Throughout these notes, the

    folder you select in figure 2 will be referred to as the „Installation Folder‟. The place

    where you later choose to put you data files is referred to as the „Database Folder‟. These can be the same as each other.

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When the installation is complete, the toolkit will consist of 2 elements:

    ? a series of .SQL queries and batch files to extract data from the Visir database.

    ? a Visual Basic tool which links to the “Visir RTDSv3.mdb” database and converts

    the extracts from Visir and PAS into the OPCDS and RTDS for radiotherapy.

The SQL queries and the batch files are located in a zip file in a folder name „Extract‟

    which can be found inside the installation folder. These files need to be moved onto the

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    VISIR system. They will produce a series of CSV files that need to be transferred to the

    PC containing the toolkit. The toolkit needs to run on a PC running Microsoft Office.

    In addition, you should take a copy of the two empty MS Access databases („Visir RTDS v3.mdb‟ and „Visir RTDS v3 Output.mdb‟) that have been placed in your installation folder

    and place them into a different, suitable folder, again this must be either on the PC you

    are running the toolkit on or a mapped drive viewable from that PC. This different folder

    will be referred to throughout as the „database folder‟. In previous versions of the toolkit,

    these files have been placed into C:\RES. You may choose to retain this practice in

    which case you can use the toolkit as before without additional action. If you choose not

    to place your data files in C:\RES, you must do the following:

    Place the CSV files in the same folder as the two database files. Open („Visir RTDS v3.mdbon the computer on which the toolkit (not the data) resides. Open the Linked Table Manager via the Tools menu and Database Utilities option.

The following screen will appear:

    Tick the “Always prompt for new location” box. It is vitally important that you only select one file at a time. You do this by placing a tick in the box adjoining it, then clicking the

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    „OK‟ button. You will be prompted for the location of this CSV file. Repeat the process

    until all files have been re-linked.

Please note: If you have already installed a previous version of the RTDS Visir Tool you

    will need to remove the software by opening the control panel and selecting add or remove programs to uninstall the RTDS VISIR Setup before installing a newer version.

The error message similar to the one shown below will appear if there is a previous

    version of the toolkit installed.

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    2. Running the extracts from Visir

VERY IMPORTANT: Do NOT run the extracts on a live database while patients are being

    treated. Use a backup server, or run them at a time when the database is not being used

    for patient treatments. There is a small risk that the database may slow or crash while

    the reports are being run.

The purpose of the batch file and queries is to copy the appropriate tables and fields from

    your VISIR system in order to create the 8 data and 5 lookup tables in the reports folder.

Please note: The extracts must be run a minimum of 10 days after the end of the time

    period to be extracted. This is to ensure data integrity, see unsummarised records in

    section 4 below.

    Instructions for using the VISIR Export files

The use of these extract files has been approved by Nucletron.

    ? Create 2 folders named SQL ad REPORTS in the VISIR base directory.

    ? The series of sql queries and batch files will be found in the „Extract‟ folder within

    the Installation Folder. You will need to copy these to the SQL folder in the VISIR

    base directory which you have just created.

    ? Open natsatextract.bat and enter 'base path', 'username' and 'password' and if

    necessary modify sql files etc accordingly.

    ? Run the natsatextract.bat files. This should take approximately 30-60 minutes

    depending on amount of data and processor power.

    ? The required output files will be returned to the reports folder which will rename

    itself with today's date when completed i.e. 13-03-2007 NCS

    ? The Fileclean.bat will run automatically as part of this process. It is used to tidy up

    the data text files i.e. removing leading and trailing ','. You may decide not to use

    this.

    ? The csv files present in the reports folder are.

    CODEDIAG

    CODEINTENTION

    CODEPRIOCAT

    CODEREGION

    CODETREATTYPE

    FIELD

    FIELDEXP

    FIELDSERI

    FRACTION

    PATIENT

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    REQUISITION

    SERIES

    TARGETVOL

    ? Copy the .csv files from the reports folder extract files from Visir into the database

    folder on your system.

    .

Please Note: The exported csv file should be left „as is‟ once exported. Don‟t attempt to

    open the file in any other package such as Microsoft Excel as this can cause corruption of

    the data.

3. Creating the extract from PAS

    A critical phase of the RTDS extraction is the production of an extract from your PAS

    system for all patients treated during the period specified.

    To assist in creating the PAS data extract, a text file can be generated containing a list of

    patient identifiers that appear in the VISIR extract between the dates specified. For

    further information please go to Step 3 of Section 4 - Running the VISIR tool.

    The format of the PAS Extract is a CSV file with the columns listed in the document

    Specification for Extract from PAS for RTDS v3.7.doc‟. It is important to note that

    although some fields are marked as optional they must still be represented in the csv file

    by using a comma. Column names do not have to match the RTDS field headings. They

    do, however, have to be included and they MUST appear in the order specified.

The extract will be required at the end of each month (in time for the submission to be

    made on the tenth of the following month) to include information for all patients attending

    for radiotherapy during the month.

See Specification for Extract from PAS for RTDS v3.7.doc for further information.

    ? Create the output file as a comma delimited file with quotes as the text identifier.

    ? Name the file “PASData.csv”

    ? Copy PASData.csv into your database folder on your system.

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    4. Running the VISIR tool

To open the VISIR tool, use the shortcut on the desktop or find the

    VISIR_RTDS_Toolkit_v2.0.x.exe file in C\RES. The Main Application Screen will appear

    as below:

Step 1 Gather Your Data

The tool will not run unless all the VISIR csv files are present.

If you have correctly placed all of the extract tables in the Database Folder, step 1 will be

    marked as complete, as shown here. Skip step 1.

    If the button “Browse for CSV File” is active and the message “CSV Files is missing. Please locate appears as below, then you need to check that the Visir extract csv files

    are in the database folder on your system and named correctly. If the extract files are in a

    different location, you can direct the tool to them by using the browse button to locate

    the missing file.

Please note the browse option will copy the CSV files from the different location into

    database folder. If you then amend the original CSV files (for example when running a

    new month‟s extract) the tool will not take account of these changes. It will still use the

    “old” copy in the database folder. This time you will not be able to redirect it back to the

    original files or browse. The copy in the database folder must be changed and the

    Refresh Data button clicked.

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If you have previously run a version of the toolkit and completed the Reference and

    Integrity checks (see Step 4 below) you will have generated data in the look-up tables of

    the back-end database (Visir_RTDS v3.mdb). If you moved this database out of the

    Installation folder prior to installing the new version you can transfer the data from these

    tables into the new version to avoid having to repeat some of the tasks. Clicking the

    „Import Look-up Data‟ button will allow you to browse for the original database. Please

    take careful note of any warning messages as data will not be imported automatically if

    the structure of the tables has changed between versions. You will have to transfer the

    data over using queries. If you do not know how to do this, contact the helpdesk on 0870

    840 8033.

    Step 2 Centre Information & Dates Information specific to your Centre needs to be recorded. This can be done by via

    following the instructions on the screens:-

    1. Select your organisation name from the drop down menu. If it is not listed, you can

    enter it in the table named “RES_Centres” in the Visir RTDS v3 database or

    telephone the RTDS Helpdesk on 0870 840 8033.

    2. Select from the option of “NHS Number or Local Patient Identifier to identify

    which field in the PAS Extract will be used to link the PAS and VISIR data.

    3. Select from the option of PersNo”, “PatID2” or “PatID3” to identify which patient

    identifier field in the VISIR system will be used in the tool to link the PAS and

    VISIR data.

    4. Enter the inclusive time period for which the extract is to be run. (This is normally

    one complete calendar month).

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    Please note: The settings above and on those in Step 4 can be saved by choosing Save and Close option when you close the tool.

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