TIBCO Spotfire Clinical 3.3 - TIBCO Product Documentation
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1. lt Addin FullTypeName Spotfire Dxp Automation Framework FrameworkAddiIn Spotfire Dxp Automation Framework gt lt AddIn FullTypeName Spotfire Dxp Automation Tasks BaseTasksAddIn Spotfire Dxp Automation Tasks gt lt Addin FullTypeName Spotfire Dxp OracleClinical Automation OracleClinicalTasksAddiIn Spotfire Dxp OracleClinical Automation gt lt AddInRegistry gt 8 17 TIBCO Spotfire Clinical 3 3 Configuring the Information Model 3 Configuring the Information Model This chapter is intended for the Data Manager Access to Oracle Clinical metadata and individual trial views is provided through a generic Information Model IM that is shipped as part of TIBCO Spotfire Clinical Import the information model and edit the data source by adding information relevant to your Oracle Clinical database in Information Designer as described below 3 1 Importing the Oracle Clinical Information Model 1 Place the OracleClinical IM part0 zip file in the Shared Disk Location on the TIBCO Spotfire Server Comment See the TIBCO Spotfire Installation and Configuration Manual for more information about the Shared Disk Location 2 Log into TIBCO Spotfire as a user with Library Administration rights 3 Select Tools gt Library Administration Response The Library Administration tool is displayed 4 Click on the Import button Response The Import dialog is displayed 5 Click Browse and select the OracleClinical IM2. Clinical information model e The licenses enabled for each end user It is very important to protect the imported Oracle Clinical information model so that it cannot be changed or tampered with by unauthorized users Assigning Folder Permissions This chapter is intended for the Data Manager Log into TIBCO Spotfire as a user that has Spotfire Administration or Library Administration rights Select Tools gt Library Administration Select the folder containing the Oracle Clinical information model you want to assign access rights to and click on the Edit link next to the Permissions for Selected Folder header Assign Access permission for those users groups that should be consumers of reports containing data from this folder Assign Browse Access Modify permission to those users Data Managers or groups containing Data Managers that should be able to use the information links when creating analysis files Comment Data Mangers responsible for setup and use of the information model and its containing entities when creating reports should be given a minimum of Browse and Access rights If Data Managers should have the possibility to edit a specific Information Model the permission should be set to Browse Access and Modify Full Control should only be given to those users who need to administrate the access to a particular Information Model e g assign the access rights to new Data Managers or revoke acces
3. if other than the default in a web browser Log in as a Spotfire Administrator Select the tab Deployment Select whether to deploy to the Production Area or to the Test Area from the View drop down list at the top of the Deployment tab Comment For more information about deployment areas and the distinction between them see the TIBCO Spotfire Deployment and Administration Manual Click the Edit button Response The deployment tab will enter edit mode Click the Add button Response The Add to Deployment dialog is displayed 6 17 TIBCO Spotfire Clinical 3 3 Installing TIBCO Spotfire Clinical 7 Click the Browse button Response A File Upload dialog is displayed 8 Browse to the SpotfireClinical Automation spk file and click Open 9 Click OK in the Add to Deployment dialog to upload and add the file to the distribution Response The list of packages is updated with the contents of the file 10 Click the Validate button in the lower right corner to make sure the deployment is not damaged or corrupted in any way 11 Click the Save button in the lower right corner to save and publish the deployment Response The Save Deployment dialog is displayed 12 Enter a version number and a description for the deployment and click the OK button For more information see the online help of the Administration Console 2 2 2 Updating Automation Services Two DLL files need to be copied to your Automation Services insta
4. S Patent No 6 014 661 and U S Patent No 7 216 116 Other patent s pending TIBCO Software Inc Confidential Information 2 17 TIBCO Spotfire Clinical 3 3 Contents 1 Introduction 4 1 1 Prerequisites 4 1 2 Roles 4 2 Installing TIBCO Spotfire Clinical 5 2 1 Deploying SpotfireClinical spk 5 2 2 Automation Services 6 3 Configuring the Information Model 9 3 1 Importing the Oracle Clinical Information Model 9 3 2 Modifying the Oracle Clinical Information Model 10 4 Configuring Access Rights 12 4 1 Assigning Folder Permissions 12 4 2 Assigning the License 13 5 Updating Clients with TIBCO Spotfire Clinical 14 6 Accessing TIBCO Spotfire Clinical 15 Appendix Information Link and Data Source Setup 16 TIBCO Spotfire Clinical 3 3 3 17 Introduction 1 Introduction TIBCO Spotfire Clinical allows end users to easily connect to Oracle Clinical OC databases and open data from one or more clinical studies in TIBCO Spotfire This document is used to help with installing and configuring the product for the end users 1 1 Prerequisites The instructions below assume that you have a working installation of TIBCO Spotfire 3 3 You must also have access to a running TIBCO Spotfire Server version 3 3 that TIBCO Spotfire will connect to How to install a Spotfire Server is described in the TIBCO Spotfire Server Installation and Configuration Manual For more information on the system requirements of TIBCO Spotfire
5. TIBCO Spottfire Clinical 3 3 Installation and Configuration Manual PD TIBCO The Power of Now Revision date 7 April 2011 Important Information SOME TIBCO SOFTWARE EMBEDS OR BUNDLES OTHER TIBCO SOFTWARE USE OF SUCH EMBEDDED OR BUNDLED TIBCO SOFTWARE IS SOLELY TO ENABLE THE FUNCTIONALITY OR PROVIDE LIMITED ADD ON FUNCTIONALITY OF THE LICENSED TIBCO SOFTWARE THE EMBEDDED OR BUNDLED SOFTWARE IS NOT LICENSED TO BE USED OR ACCESSED BY ANY OTHER TIBCO SOFTWARE OR FOR ANY OTHER PURPOSE USE OF TIBCO SOFTWARE AND THIS DOCUMENT IS SUBJECT TO THE TERMS AND CONDITIONS OF A LICENSE AGREEMENT FOUND IN EITHER A SEPARATELY EXECUTED SOFTWARE LICENSE AGREEMENT OR IF THERE IS NO SUCH SEPARATE AGREEMENT THE CLICKWRAP END USER LICENSE AGREEMENT WHICH IS DISPLAYED DURING DOWNLOAD OR INSTALLATION OF THE SOFTWARE AND WHICH IS DUPLICATED IN LICENSE_TIBCOSPOTFIRECLINICAL PDF OR IF THERE IS NO SUCH SOFTWARE LICENSE AGREEMENT OR CLICKWRAP END USER LICENSE AGREEMENT THE LICENSE S LOCATED IN THE LICENSE FILE S OF THE SOFTWARE USE OF THIS DOCUMENT IS SUBJECT TO THOSE TERMS AND CONDITIONS AND YOUR USE HEREOF SHALL CONSTITUTE ACCEPTANCE OF AND AN AGREEMENT TO BE BOUND BY THE SAME This document contains confidential information that is subject to U S and international copyright laws and treaties No part of this document may be reproduced in any form without the written authorization of TIBCO Software Inc TIBCO and Spotfire are either
6. ated with the contents of the file TIBCO Spotfire Clinical 3 3 5 17 Installing TIBCO Spotfire Clinical 10 11 12 2 2 2 2 1 Click the Validate button in the lower right corner to make sure the deployment is not damaged or corrupted in any way Click the Save button in the lower right corner to save and publish the deployment Response The Save Deployment dialog is displayed Enter a version number and a description for the deployment and click the OK button For more information see the online help of the Administration Console Automation Services If you have access to TIBCO Spotfire Automation Services you must also deploy the SpotfireClinical Automation spk file to the Spotfire server Use the Administration Console to deploy the file as described below When all steps below have been performed it will be possible to add a Replace Oracle Clinical Data job in the Automation Services Job Builder Note SpotfireClinical Automation spk should only be deployed when using TIBCO Spotfire Clinical together with TIBCO Spotfire Automation Services Deploying this package on a server without Automation Services will result in an error Deploying the Automation Services Package To deploy TIBCO Spotfire Clinical for Automation Services to the server Open the Administration Console located at http spotserver port spotfire where spotserver is the name of one of your Spotfire servers and port is the port number
7. llation Spotfire Dxp OracleClinical Automation dll and Spotfire Dxp OracleClinical dll gt Tocopy the DLL files 1 Locate the AutomationServices folder of the downloaded and unzipped TIBCO Spotfire Clinical package 2 Copy Spotfire Dxp OracleClinical Automation dll and Spotfire Dxp OracleClinical dll to the bin folder of your Automation Services installation on your server e g C Program Files x86 TIBCO Automation Services 3 3 webroot bin You also need to add a line of text to the AddIns xml file on the server where Automation Services is installed gt To edit the Addins xml file 1 On the Automation Services server locate the bin folder e g C Program Files x86 TIBCO Automation Services 3 3 webroot bin 2 Open the file AddIns xml in a text editor and add the following line to the lt AddIn Registry gt section lt AddIn FullTypeName Spotfire Dxp OracleClinical Automation OracleClinicalTa sksAddiIn Spotfire Dxp OracleClinical Automation gt TIBCO Spotfire Clinical 3 3 7 17 Installing TIBCO Spotfire Clinical When finished your AddIns xml file should look something like this lt xml version 1 0 encoding utf 8 gt ehees This is the AddIns xml file which must be deployed together with the AS assembly in the Automation Services directory gt lt AddiInRegistry xmlns http www spotfire com schemas AddInRegistry1l 0 xsd SchemaVersion 1 0 gt lt namespace assembly gt
8. nical package to a folder on your local disk TIB_spotclinical_3 3 0_win zip The zip file includes this PDF document release notes the deployment files SpotfireClinical spk see below and SpotfireClinical Automation spk as well as the template information model OracleClinical IM part0 zip 2 1 Deploying SpotfireClinical spk Use the Administration Console to deploy the SpotfireClinical spk file as described below gt To deploy TIBCO Spotfire Clinical to the server 1 Open the Administration Console located at http spotserver port spotfire where spotserver is the name of one of your Spotfire servers and port is the port number if other than the default in a web browser 2 Loginas a Spotfire Administrator 3 Select the tab Deployment 4 Select whether to deploy to the Production Area or to the Test Area from the View drop down list at the top of the Deployment tab Comment For more information about deployment areas and the distinction between them see the TIBCO Spotfire Deployment and Administration Manual 5 Click the Edit button Response The deployment tab will enter edit mode 6 Click the Add button Response The Add to Deployment dialog is displayed 7 Click the Browse button Response A File Upload dialog is displayed 8 Browse to the SpotfireClinical spk file and click Open 9 Click OK in the Add to Deployment dialog to upload and add the file to the distribution Response The list of packages is upd
9. odel Comment The Oracle Clinical data source template is distributed with user authentication turned on but this can be changed if necessary 6 If desired modify the Credentials timeout setting Comment Credentials are always cached for the remainder of a client session but the server side cache settings can be modified In the Oracle Clinical Data Source Template the default server side credentials caching has been set to 0 25 hours This means that if a user authenticates against an Oracle Clinical instance and then restarts the client within 15 minutes he she will not be re prompted for Oracle Clinical credentials If he she waits more than 15 minutes before restarting the client he she will be required to authenticate again Increase or decrease the number to specify how long the server should save the user credentials before requiring another login to the data source See the Data Source Tab topic in the online help of TIBCO Spotfire for more information about the Credentials timeout setting 7 Save the data source 8 If you use more than one Oracle Clinical instance you need to repeat steps 2 7 and modify the data source created for each instance TIBCO Spotfire Clinical 3 3 11 17 Configuring Access Rights 4 4 1 Configuring Access Rights The access to clinical data in TIBCO Spotfire is controlled by two different things in addition to the data source authentication e The folder permissions to the Oracle
10. part0 zip file 6 Click OK 7 Select whether or not to Include permissions If you do not include any permissions the imported content will inherit the permissions of the destination folder Comment In most cases you will probably need to modify the permissions after the import is done to fit your current user structure 8 Select Automatically assign new name or GUID to imported item to generate new identifiers for potential name and or GUID conflicts and click OK Comment This is especially important if multiple Oracle Clinical information models are being used since you will overwrite a previously added Oracle Clinical information model if conflicts are left unhandled Response The Select Destination Folder dialog is displayed TIBCO Spotfire Clinical 3 3 9 17 Configuring the Information Model 3 2 10 11 Browse to the folder where you wish to import the Oracle Clinical information model or create a new folder then click OK Comment Typically this folder would have the same name as the Oracle Clinical database this information model should be connected to Comment Access to individual data sources are handled by the regular Library access control so make sure that the folder permissions for the selected folder is sufficient for the intended end users Click Close when the status messages states Import done Comment You can click Refresh to update the status messages in the dialog or just wait
11. potfire Clinical is set up to filter out some views from the list of available views since they are normally of no interest to an end user To add more views to be filtered out or to remove a filter use the Information Designer and modify the VIEWS information link or the VIEW_NAME column element Note that modifications can only be done on a per Oracle Clinical database connection level i e the same filter condition will apply to all users of this particular data source Modifications cannot be customized on a per user group level If that type of behavior is desirable then you need to import set up and configure another generic Oracle Clinical information model to point to the same Oracle Clinical database but with a modified filter condition See Modifying the Oracle Clinical Information Model on page 10 TIBCO Spotfire Clinical 3 3 17 17
12. registered trademarks or trademarks of TIBCO Software Inc and or subsidiaries of TIBCO Software Inc in the United States and or other countries All other product and company names and marks mentioned in this document are the property of their respective owners and are mentioned for identification purposes only This software may be available on multiple operating systems However not all operating system platforms for a specific software version are released at the same time Please see the readme txt file for the availability of this software version on a specific operating system platform THIS DOCUMENT IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE OR NON INFRINGEMENT THIS DOCUMENT COULD INCLUDE TECHNICAL INACCURACIES OR TYPOGRAPHICAL ERRORS CHANGES ARE PERIODICALLY ADDED TO THE INFORMATION HEREIN THESE CHANGES WILL BE INCORPORATED IN NEW EDITIONS OF THIS DOCUMENT TIBCO SOFTWARE INC MAY MAKE IMPROVEMENTS AND OR CHANGES IN THE PRODUCT S AND OR THE PROGRAM S DESCRIBED IN THIS DOCUMENT AT ANY TIME Copyright 1996 2011 TIBCO Software Inc ALL RIGHTS RESERVED THE CONTENTS OF THIS DOCUMENT MAY BE MODIFIED AND OR QUALIFIED DIRECTLY OR INDIRECTLY BY OTHER DOCUMENTATION WHICH ACCOMPANIES THIS SOFTWARE INCLUDING BUT NOT LIMITED TO ANY RELEASE NOTES AND READ ME FILES TIBCO Spotfire is covered by U
13. s rights of people who should no longer be part of a particular clinical trial When you are done click OK to close the Folder Permissions dialog Make sure that steps 3 7 are performed for all added information models then click Close 12 17 TIBCO Spotfire Clinical 3 3 4 2 Configuring Access Rights Assigning the License This chapter is intended for the Spotfire Admin The Open Oracle Clinical Data function gives access to the Add Oracle Clinical Data wizard which gives easy access to Oracle Clinical data through the Add Data Tables tool as well as the Replace Oracle Clinical Data wizard No users or groups will have this license enabled upon installation It must be enabled by following the steps below Note Only those users who will create reports need to have the TIBCO Spotfire Clinical license enabled Consumers of reports based on clinical data do not need a specific license To assign the licence Log into TIBCO Spotfire as a user with Administration privileges Select Tools gt Administration Manager Go to the Groups and Licenses tab and select the group for which to enable the TIBCO Spotfire Clinical license Comment Licenses are always assigned to groups never to individual users On the Licenses tab click Edit Assign the license by selecting the check boxes for the TIBCO Spotfire Clinical license group and for the underlying Open Oracle Clinical Data function Repeat steps 3 5 for all group
14. s that should have access to the Add Oracle Clinical Data functionality TIBCO Spotfire Clinical 3 3 13 17 Updating Clients with TIBCO Spotfire Clinical 5 Updating Clients with TIBCO Spotfire Clinical When the spk file has been deployed to the Spotfire Server you must perform some additional steps to update the Spotfire clients Note that these steps must be performed on all computers running Spottfire gt To update the Spotfire Client 1 Exit TIBCO Spotfire 2 Restart TIBCO Spotfire and log in as usual You will be notified that there are new packages deployed on the server Accept the updates to download and install the new packages 14 17 TIBCO Spotfire Clinical 3 3 Accessing TIBCO Spottire Clinical 6 Accessing TIBCO Spotfire Clinical First access to the clinical data is supplied through File gt Add Data Tables In the Add Data Tables dialog you can select one or multiple data tables to be added in a single step For end users with access to the Open Oracle Clinical Data function the Oracle Clinical Data option will show up in the Add drop down list in the Add Data Tables dialog See the TIBCO Spotfire User s Manual or the online help for more information about Add Data Tables Replace a previously added Oracle Clinical study by selecting File gt Replace Oracle Clinical Data There is no need for any deployment on the TIBCO Spotfire Web Player server Users of the Web Player will be able
15. see http spotfire tibco com sr There must be at least one Oracle Clinical instance available with data from one or more studies 1 2 Roles Spotfire defines different roles for installing configuring and administering the different components of the system e Spotfire Server Administrator This role is responsible for installing and configuring the Spotfire Server s and the Spotfire database How to perform these tasks is described in the TIBCO Spotfire Server Installation and Configuration Manual e Spotfire Admin This role is responsible for setting up users and groups in the Spotfire system assigning licenses and preferences to the Spotfire groups setting up the Spotfire Library and deploying Spotfire software packages to the Spotfire Server How to perform these tasks is described in the TIBCO Spotfire Deployment and Administration Manual e Data Manager This role is responsible for setting up data sources and elements in Information Designer so that the correct data becomes available for the end users These roles can be assigned to different persons or to the same person It is important that the person or persons assuming the roles are familiar with each respective area of knowledge 4 17 TIBCO Spotfire Clinical 3 3 Installing TIBCO Spotfire Clinical 2 Installing TIBCO Spotfire Clinical This chapter is intended for the Spotfire Admin Start by unzipping the downloaded TIBCO Spotfire Cli
16. ting the list of views in a study It should have two columns ISYS ALL_VIEWS OWNER not retrieved with a single value prompt SYS ALL_VIEWS VIEW_NAME retrieved with a filter 1 NOT IN RDCMS_VIEW RESPONSES_VIEW The property OracleClinical QueryType should be set to VIEWS Data Source The data source must be configured with the following open session commands ALTER SESSION SET NLS_NUMERIC_CHARACTERS The information model distributed with TIBCO Spotfire Clinical includes the required elements pointing to a generic data source When making the modifications described in section 3 2 above you should automatically end up with a working set of elements and information links 16 17 TIBCO Spotfire Clinical 3 3 Accessing TIBCO Spottfire Clinical Note that the data source template assumes that you have access to the Oracle native driver If this should not be the case you can modify the Type of the data source to use DataDirect instead gt To use the Oracle DataDirect driver instead of the Oracle native driver 1 Right click on the data source you want to change and select Edit from the pop up menu 2 Change the data source Type from Oracle to Oracle Data Direct 3 Edit the Connection URL 4 Make sure the Open session command is set to ALTER SESSION SET NLS_NUMERIC_CHARACTERS 5 Save the data source Changing the Available Views The information model distributed with TIBCO S
17. to connect to the clinical data directly once the analysis has been set up With TIBCO Spotfire Automation Services you can include the task Set Data Source Credentials in any automated job where data source authentication is required TIBCO Spotfire Clinical 3 3 15 17 Accessing TIBCO Spottfire Clinical Appendix Information Link and Data Source Setup For every Oracle Clinical database two information links are set up These information links contain the queries used for finding studies and views respectively and the results are used to populate the Add Oracle Clinical Data user interface The Add Oracle Clinical Data wizard will find the database by doing a search in the library for information links with the OracleClinical QueryType property set That way library permissions can control which users and groups see which databases Information Links The information links are set up using the following specification 1 One information link is used for extracting the list of studies each end user has access to It should include two columns RXC STUDY_ACCESS_ACCOUNTS STUDY_ACCESS_ACCT_NAME RXC USER_STUDIES STUDY not retrieved Two inner joins are needed RXC STUDY_ACCESS_ACCOUNTS CLINICAL_STUDY_ID RXC_DES CLINICAL_STUDIES CLINICAL_STUDY_ID RXC USER_STUDIES STUDY RXC_DES CLINICAL_STUDIES STUDY The property OracleClinical QueryType should be set to STUDIES 2 One information link is used for extrac
18. until all messages are shown and the import is finished If you use more than one Oracle Clinical database you need to repeat steps 4 10 and import the information model once for each instance Comment You can also make a copy of the imported information model template and make the modifications described below on each copy Modifying the Oracle Clinical Information Model Select Tools gt Information Designer Response The Information Designer is displayed In the Data Sources pane right click on the newly imported data source named Oracle Clinical Data Source Template and select Edit Comment Note that you must not change the Open session commands supplied with the template these commands are required by Oracle Clinical to set up the connection see also the Data Source section on page 13 Change the Name of the data source e g to the name of your Oracle Clinical database Comment This name will be shown to the end users when adding Oracle Clinical data to an analysis and it is used to distinguish between multiple instances of Oracle Clinical data sources Provide a Connection URL a Username and a Password to your Oracle Clinical database Comment This is required in order to save the data source even if you intend to apply user authentication on the data source If desired change the User authentication setting for the data source 10 17 TIBCO Spotfire Clinical 3 3 Configuring the Information M
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