JMP to LSAF Add-in. User Guide v1.1

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1 JMP to LSAF Add-in User Guide v1.1

2 Table of Contents Terms and Conditions... 3 System Requirements... 3 Installation... 3 Configuration... 4 API Setup... 4 Java Configuration... 5 Logging In... 5 Launching the Add-in... 5 Adding a Login Configuration... 6 Preferences... 6 Folder Locations... 6 Default Programs... 7 SAS Session... 7 General Usage (Repository and Workspace)... 8 Buttons and Navigation... 8 Object Type Icons... 8 Context Menu Items Shared by Repository and Workspace... 9 Repository... 9 Repository Context Menus... 9 Workspace Workspace Context Menus LSAF SAS Editor Opening a SAS Program Running a SAS Program Saving a SAS Program Local SAS Session Editor Opening a SAS Program General Usage Buttons Reports Dashboard Opening the Reports Dashboard Tab... 12

3 Creating a New Report Dashboard Entry Editing a Report Dashboard Entry Status Icons Updating a Report Exporting and Importing Reports Dashboard Entries Other Other Notes... 16

4 Terms and Conditions SAS INSTITUTE INC. IS PROVIDING YOU WITH THE COMPUTER SOFTWARE CODE INCLUDED WITH THIS AGREEMENT ("CODE") ON AN "AS IS" BASIS, AND AUTHORIZES YOU TO USE THE CODE SUBJECT TO THE TERMS HEREOF. BY USING THE CODE, YOU AGREE TO THESE TERMS. YOUR USE OF THE CODE IS AT YOUR OWN RISK. SAS INSTITUTE INC. MAKES NO REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT AND TITLE, WITH RESPECT TO THE CODE. The Code is intended to be used solely as part of a product ("Software") you currently have licensed from SAS Institute Inc. or one of its subsidiaries or authorized agents ("SAS"). The Code is designed to either correct an error in the Software or to add functionality to the Software, but has not necessarily been tested. Accordingly, SAS makes no representation or warranty that the Code will operate errorfree. SAS is under no obligation to maintain or support the Code. Neither SAS nor its licensors shall be liable to you or any third party for any general, special, direct, indirect, consequential, incidental or other damages whatsoever arising out of or related to your use or inability to use the Code, even if SAS has been advised of the possibility of such damages. Except as otherwise provided above, the Code is governed by the same agreement that governs the Software. If you do not have an existing agreement with SAS governing the Software, you may not use the Code. System Requirements The following are required to run the JMP to LSAF add-in: JMP 13 Java 1.6+ SAS Drug Development or SAS Life Science Analytics Framework API Windows 7+ Installation For customers installing the JMP to LSAF add-in for JMP or JMP Pro 12 or higher, reference these links: JMP 12 Installation Notes JMP 13 Installation Notes For customers installing the JMP to LSAF add-in for JMP Clinical 6.0, reference this link: Installation Instructions for JMP Clinical 6.0 For customers installing the current version of Java, reference this link: Java Help Center - Installing Java Information on installing JMP add-ins can be found here: JMP Add-Ins

5 Configuration API Setup Once the add-in is installed, follow the steps below to download and configure the Java API 1. Determine the necessary Java API version using the link below Usage Note 58433: SAS Drug Development API Macros - Get instance Java API and API Macro versions 2. Download appropriate Java API version from one of the two links below. SAS Drug Development: Installation Note 46609: SAS Drug Development 4 - Accessing Java API all versions client and macro downloads SAS Life Science Analytics Framework: Installation Note 57862: SAS Life Science Analytics Framework - Accessing Java API all versions client and macro downloads 3. In JMP, click View > Add-Ins. Select JMP to LSAF Add-in from the List Box. 4. Click on the link to the Home Folder. 5. Double-click on the Java folder 6. Double-click on the lib folder 7. Extract the downloaded zip file containing the Java API 8. Copy the.jar files from the lib folder (within the extracted folder) 9. Paste the.jar files to the lib folder within the add-ins directory, as shown below

6 Java Configuration This is only necessary if you have multiple versions of Java installed and the default version does not match the current version stored in the registry. This will cause the add-in to fail to launch and the steps below are needed. 1. In JMP, click View > Add-Ins. Select JMP to LSAF Add-in from the List Box. 2. Click on the link to the Home Folder. 3. Double-click on the Tables folder 4. Open the Java Path.jmp table 5. Change the value JAVA.EXE in the Path column to be a full path to a Java executable. Logging In Launching the Add-in 1. Select the JMP to LSAF Add-in from the Add-Ins menu. 2. Login window will appear.

7 Adding a Login Configuration 1. After launching the add-in, click the green plus sign button to add an instance URL for SAS Drug Development or Life Science Analytics Framework. After adding URL and username, click OK to save this configuration. Note: the above entries are examples that are used throughout this document. The dialog is initially blank. 2. After the configuration is added, the new URL will be selected and you can type in your password to login. The X button removes instances as needed. Preferences Folder Locations Set the local download folder location for downloaded files by clicking the Folder icon.

8 Default Programs Set the default program that the add-in uses to download Files. SAS Session Set preferences for the JMP LSAF SAS Session Editor. Below are the default values.

9 General Usage (Repository and Workspace) Buttons and Navigation Once connected, users can drill down into the folder structure and use the following functionality in the Repository and Workspace Navigation Button Action Navigate up one level within the tree structure Navigate up one or more levels above the current directory Navigate to a known location (after typing or pasting location in the navigation bar) Refresh the current directory Actions Button Action Create folder Upload files, upload and expand zip files, and upload report windows Download files and download as a ZIP file Open the Reports Dashboard (Repository Only) Open the Preferences window Copy the path of the current directory to the clipboard Object Type Icons Icon Object Type Organization Users Container Project Analysis Files Container Folder File SAS Program

10 SAS Data Set LSAF Job PDF Context Menu Items Shared by Repository and Workspace There are several context menu items that exist in both the Repository and Workspace tabs. They are as follows: Make File Info Into Data Table Creates a JMP Data Table containing the current folder/containers file metadata Open With LSAF SAS Session Open a SAS Program in the JMP LSAF SAS Editor Open With Local SAS Session Open a SAS Program in the JMP Local SAS Session Editor Open With JMP Open a file using JMP Open With OS Default Open a file using the Operating System s default setting Upload Upload Files Upload one or more files Upload Upload and Expand Upload a zip file and expand Download Download Download the selected file(s) Download Download As Zip Download the selected file(s) into as a zip file Rename Rename an object Delete Delete an object Run Run an LSAF Job Repository Repository Context Menus New Folder Create a new folder within the current directory in the Repository Enable Versioning Enable versioning of a single file Disable Versioning Disable versioning of a single file Check Out Check out a single file Check In Check in a single file Undo Checkout Undo the checkout of a single file Lock File Lock a single file Unlock File Unlock a single file Version History View the version history of a file Audit history View the audit history of an object Copy To Workspace Copy Latest Version Copy the latest version of a file to the Workspace Copy To Workspace Copy Specific Version Copy a specific version of a file to the Workspace Properties View all attributes of a single file Copy Path Copy the path to a single object Refresh Repository Refresh the contents of the current directory in the Repository

11 Workspace Workspace Context Menus New Folder Create a new folder in the current directory of the Workspace New SAS Program Create a new SAS Program in the current directory within the Workspace Mark For Addition and Check In Mark a single file for addition and check it into the Repository Refresh Workspace Refresh the contents of the current directory in the Workspace LSAF SAS Editor Opening a SAS Program If the default program preference is set to LSAF SAS Editor, a SAS program can be opened in the editor by double clicking. Otherwise, use the context menu (Open With LSAF SAS Session) to override preferences and open with the LSAF SAS Editor. When opening a SAS program from the Repository, the file will be read-only and cannot be submitted. When opening a SAS program from the Workspace, the file can be edited and saved back to the Workspace. The program can also be submitted through a temporary LSAF Job. Running a SAS Program SAS programs opened from the Workspace can be submitted to LSAF by clicking the Run button. When a SAS program I submitted, the following events take place: 1. The current SAS program is saved back into the Workspace. 2. An LSAF Job is created in the Workspace. This job contains the path to the current SAS program in the Workspace. The location and name of this Job is controlled by the SAS Session preferences. 3. The newly created job is submitted. 4. The Add-in waits until the job has completed. 5. The log and listing files are retrieved. The log is appended and the lst file replaces the content in the Output tab. Saving a SAS Program SAS programs opened from the Workspace can be saved back to the Workspace by clicking the Save button. A confirmation message will appear if the save is successful, as shown below.

12 Local SAS Session Editor Opening a SAS Program Use the context menu (Open With LSAF SAS Session) to open a SAS Program with the LSAF SAS Editor. If a SAS connection is already established, the Local SAS Session tab will automatically load. If there is not an existing connection, there is a prompt to connect to SAS. JMP can connect to SAS locally or on a remote server. General Usage Buttons Section Libraries Results Code Editor Log Output Button Details View current library references. Open a table by expanding a library and doubleclicking on the data set. View past result files. This will contain ODS output created by the JMP Generated code as well as ODS output by non-jmp generated code. NOTE: Turning of JMP ODS is not supported in the add-in at this time. Edit SAS Programs opened from LSAF or from the local file system. Additionally, creating new SAS Programs that are not saved locally is supported. NOTE: Running code using this editor causes macro variables typically created by LSAF (i.e. _SASWS_) to be unavailable. The log is appended after each submission. The output is replaced after each submission. Action Open a SAS Program from the local file system Save the current SAS Program to the local file system Submit the current SAS Program using the current SAS Connection Open the folder containing the current SAS Program in Windows Explorer Create a new SAS Program Create a new library reference Refresh the Library Pane NOTE: The Local SAS Session editor is only available on JMP 13+.

13 Reports Dashboard Opening the Reports Dashboard Tab 1. Click the Reports Dashboard icon from the Repository Creating a New Report Dashboard Entry 1. Click the green plus sign button to add a new entry 2. Give the report a name. This must be unique of your list of reports. 3. Paste Repository paths to the output report and the JSL file path. (Use the right click context menu > Copy Path to easily copy the path to a file.

14 4. Select the type of report (PDF or HTML) 5. Click green plus icon to add a data source for the report. 6. Paste path to data source and click OK

15 7. Click OK to create Report Dashboard entry Editing a Report Dashboard Entry You can edit a report entry by double clicking on the report in the dashboard, or clicking the Edit Report button.

16 Status Icons Icon Object Type The report is newer than all data sources. The report is older than at least one data source. The report file does not exist or there was an error while retrieving the modification date for either the report or data source(s). Updating a Report You can update a report by clicking the Run button. Updating a report does the following: 1. Downloads all data sources and the JSL script 2. Opens the data sources in JMP 3. Runs the JSL script 4. Saves the last report window created as a PDF or HTML file 5. Closes the report window 6. Uploads the saved file to the Repository at the Report Path Exporting and Importing Reports Dashboard Entries Export dashboard entries by clicking the Export button. Select the reports to be exported and click OK. There will be an additional prompt for saving the exported file. Import dashboard entries by clicking the Import dashboard entries from the exported file. button. Select an exported file to create new Other Sorting Right-click the header of the table and click Sort By Column

17 Filtering Type filter criteria in text box and click the Filter button Uses Contains operation on the Report Name fields only Previewing Reports Click on a report entry within the table to preview in the Preview Pane This preview action will download the report every time you select a report to allow previewing To turn off previewing, slide the preview pane to the bottom of the window Other Notes Connections time out at the default of 30 minutes. To increase this time, a configuration change on the server is required. The expired session error dialog box looks like this:

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