Appendixes | Configuring JMP Clinical

Configuring JMP Clinical
JMP Clinical supports multiple configurations that can define a distinct set of folders where study metadata and report output is stored. One of the main purposes of this feature is to enable sharing of studies and reviews (at varying levels) using shared (or mapped) network drives across a set of users.
Configuration Files
Three main files are shipped with JMP Clinical and exist in the product install directory ( C:\Program Files\SASHome\JMPClinical\12\LifeSciences ) to control configurations, path preferences, and system preferences.
installation.configuration.preferences
The installation.configuration.preferences file contains named configuration variations and the root location(s) to look for installation configurations (as defined by the installation.path.preferences file described below). This file should always remain in the installation directory and is used to surface options in the JMP Clinical Main > Settings > Configuration pane to change configurations.
installation.path.preferences
The installation.path.preferences file contains all the path locations that can be configured to change where JMP Clinical reads and writes for system operations. The Default "Local" configuration shipped with the product looks for this file in the install directory. All default paths use a local configuration and store metadata under the JMP Clinical application data USER ROAMING profile ( C:\Users\^USER^\AppData\Roaming\SAS\JMPClinical\12 ).
To set up a new configuration, this file must be copied and placed into the target root directory location as specified in installation.configuration.preferences.
To successfully set up a new configuration, at a minimum we recommend changing the path specifications in the following lines of the file placed in the share root directory.
{"<userRoot>", "$HOME"} where $HOME should be changed to reference the root path of the configuration
{"/system/clinical/preferences", "$LS_HOME"} where $LS_HOME should be changed to reference the root path of the configuration (or another location of your choice)
{"<userLocal>", "$DOCUMENTS\JMPClinical\Local"} where "Local" should be changed to reference the name of the share
system.clinical.preferences
The system.clinical.preferences file contains various system-level options for a given configuration. This file should also be copied and placed in the target location specified for the "/system/clinical/preferences" key in installation.path.preferences.
One of the key components of the system.clinical.preferences file is the specification of user role assignments. A user role defines the level of functional interactivity that a user has in JMP Clinical. The following user roles can be set for individual users.
Study Manager - A user with this role can do all of the operations involved in managing studies within JMP Clinical: add, combine, and refresh metadata, rename or move folders, update a review with a new snapshot, update the study risk data set, and delete studies. The code specification for this role is "StudyManager" .
Review Author - A user with this role can create/edit/save Review Templates, do ad hoc analyses, and create and save Reviews. They can also manage the Holiday and Event data set and Risk Threshold data sets used by the configuration. A Review Author implicitly has the Reviewer role as well. The code specification for this role is "ReviewerAuthor" .
Reviewer - A user with this role can open Reviews. The code specification for this role is "Reviewer" .
Settings Editor - A user with this role has access to the Settings tab on the Main Clinical . This enables them to select different configurations (if defined), and change how they view Documentation and Help. The code specification for this role is "SettingsEditor" .
Important Note: We generally do not recommend restricting the "SettingsEditor" rights from users. This should be done only if you want to severely restrict the use of the system for that user such that they are not able to select configurations.
By default, all users are assigned all roles. System administrators, however, can restrict individual users to specific user roles using the following procedures. See Setting Up an Alternate Configuration for information about specifying user roles.
Controlling System Preferences for a Configuration
System preferences are specified in the system.clinical.preferences file. Use a text editor to make changes. Be sure not to alter the original syntax, which is of the following form:
/*** Comment about preference group ***/
{“PreferenceKey”, PreferenceValue},
Note the optional comment enclosed by /*** ***/ , the left and right braces ( {} ) enclosing the key-value pair, the key enclosed in double quotation marks ( “” ), the comma ( , ) after the key, the value (the presence of enclosing quotation marks or braces varies depending on its type), and the comma following the enclosed key-value pair unless it is the final key-value pair in the file.
Restart JMP Clinical after you save your changes to this file. Preferences are described below.
Check for JMP Clinical Updates
1 - Automatically check at start-up. If updates are found, a notification is shown on the Settings > About JMP Clinical pane.
0 - Disable automatic checks at start-up. You can manually check for updates using Settings > About JMP Clinical > Check for Updates button.
Documentation Download URL
Study Management Options
1 - When a study is deleted, do not delete notes or reviews associated with it. Choose this option to preserve study artifacts when you do not anticipate using the same study name in the future.
0 - When a study is deleted, delete notes and reviews associated with it.
Lock File Options
A study management lock is a temporary restriction imposed on users to prevent conflict with an ongoing study management operation (for example, adding, combining, refreshing, renaming, and deleting studies). Under normal circumstances, these locks are removed automatically when the study management operation is complete. Operations on very large studies generally take more time. Exceptional system events might prevent the operation from completing, keeping the lock in effect.
0 ... 1e+308 , with fractional hours permissible.
A study usage lock is a temporary restriction imposed on users to prevent conflict with an ongoing study usage operation (for example,, running reports in Review Builder). Under normal circumstances, these locks are removed automatically when the study usage operation is complete. A user leaving Review Builder open, as well as exceptional system events, might keep the lock in effect.
0 ... 1e+308 , with fractional hours permissible.
Review Options
1 - Wait until a report tab is given focus before loading its content. This is particularly useful when manipulating very large reviews on slower machines, as it divides and shifts the load penalty into individual reports.
0 - Load all content from all report tabs at once, when the review is opened. All loading is done in one operation.
1 - Ensure that the creation date of a study found on disk matches the creation date of an identically named study recorded in the review, before using the study for any subsequent operations.
0 - Allow a study on disk with the same name but different creation date as a study referenced in a review, to be considered as a valid match for use in subsequent operations. Choose this option for greater flexibility if the creation date safeguard is not needed for your work environment.
1 - Ensure that the update date of a study found on disk matches the update date of an identically named study recorded in the review, before using the study for any subsequent operations.
0 - Allow a study on disk with the same name but different update date as a study referenced in a review, to be considered as a valid match for use in subsequent operations. Choose this option for greater flexibility if the update date safeguard is not needed for your work environment.
1 - Ensure that the snapshot number of a study found on disk matches the snapshot number of an identically named study recorded in the review, before using the study for any subsequent operations.
0 - Allow a study on disk with the same name but different snapshot number as a study referenced in a review, to be considered as a valid match for use in subsequent operations. Choose this option for greater flexibility if the snapshot number safeguard is not needed for your work environment.
1 - Show a detailed warning notification if the review template specifies options that are not available for the current study. Offending and replacement values are shown, and offending values are replaced as needed.
0 - Do not show a warning notification if the review template specifies options that are not available for the current study. Offending values are replaced as needed.
1 - Reviewers are allowed to view the report data tables. The Show Tables action button is available for this purpose, on applicable reports.
0 - Reviewers are not allowed to view the report data tables.
Specifies whether to make the JMP button available on the JMP Clinical Main . This button surfaces the JMP Home , which allows easy access to core, non-Clinical specific, JMP functionality.
1 - The JMP access button appears on the JMP Clinical Main .
0 - The JMP access button does not appear on the JMP Clinical Main .
1 - Icon only: Label report tabs with an icon only. This is the most compact labeling option.
2 - Label only: Label report tabs with a text label only. This takes up more horizontal space than an icon.
3 - Icon and label: Label report tabs with both an icon and a text label. This is the least compact labeling option.
SDD Integration Options
1 - Enable integration with SDD.
0 - Disable integration with SDD.
3.x - Connect to SDD version 3.x
4.x - Connect to SDD version 4.x
URL : The URL used to connect to an SDD instance (for example,, https://server/sdd ).
Role Assignments
Any combination of the following: StudyManager , ReviewAuthor , Reviewer , and SettingsEditor . Refer to system.clinical.preferences for a description of each of these roles.
Any combination of the following: StudyManager , ReviewAuthor , Reviewer , and SettingsEditor . These unmodified values indicate that a user gains a role beyond the defaults (specified in DefaultRoleAssignment ). Each of these values can alternatively be modified by prepending them with a minus sign ( - ) to indicate that a user loses a default role. Refer to system.clinical.preferences for a description of each of these roles.
Refer to Setting Up an Alternate Configuration for additional user role discussion and examples.
Controlling File Path Preferences for a Configuration
File preferences are specified in the installation.path.preferences file. Use a text editor to make changes. Be sure not to alter the original syntax, which is of the following form:
{“PathKey”, “PathValue”},
Note the braces ( {} ) enclosing the key-value pair, the key enclosed in double quotation marks ( “” ), the comma ( , ) after the key, the value enclosed in double quotation marks, and the comma following the enclosed key-value pair unless it is the final key-value pair in the file.
Restart JMP Clinical after you save your changes to this file. Preferences are described below.
Header and Wildcard Definitions
<USER> becomes dynamically replaced by the user name.
<STUDY> becomes dynamically replaced with the relevant study name.
Specifies the location of the system.clinical.preferences file.
/installation Paths
These path keys refer to folders within the JMP Clinical installation location (typically in Program Files ). In almost all circumstances, you are strongly advised not to modify their values.
/user Paths
These path keys refer to the user folders created while running JMP Clinical. In most cases, you should not need to change these values, but the most likely values that you might want to change are for the /user/clinical/notes (notes), /user/clinical/output (output), /user/clinical/reviewtemplates (review templates), and /user/clinical/reviews (reviews) keys. For example, you might decide that each user maintains their own study list (on the ‘same’ set of studies) but that notes, review templates, and reviews should be shared amongst all users. Where location changes are desired, you are encouraged to use path wildcards (see Header and Wildcard Definitions ) to reduce future maintenance, should these locations change again.
Templates used by the Adverse Events Narrative report.
You can add, modify, or remove path wildcard keys (for example,, <userLocal> ) and values, so long as no subsequent path values refer to undefined keys. However, you must not add, modify, or remove standard keys (for example, /user/clinical/notes ) -- you can only modify their values.
Path Resolution Examples
For demonstration purposes, pretend that your user name is zzsmith , and your current study is named Nicardipine . $HOME and $DOCUMENTS are reserved JMP path variables that refer to two different user-specific locations. <STUDY> is a reserved JMP Clinical wildcard that refers to the current study. Keys, values, and corresponding example resolved values are shown below.
Example Resolved Value 1

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Your value resolution might differ depending on your operating system configuration, environment and path variable definitions, and user-defined JMP Clinical path wildcard definitions made elsewhere in installation.path.preferences .

Setting Up an Alternate Configuration
Map the shared or network drive and set up the shared folder.
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In this example, the shared drive is defined as drive U: . Note : Your file path will be different.
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In this case, we will name the folder ClinicalShare . This folder will serve as the root directory for the new shared configuration.
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Copy the installation.path.preferences and the system.clinical.preferences files from the product install directory ( C:\Program Files\SASHome\JMPClinical\12\LifeSciences ) into the ClinicalShare folder.
Note : For simplicity, these instructions will use the same ClinicalShare location for placing the system.clinical.preferences file. This file could be placed in a separate location for a system administrator to manage.
Modify the installation.configuration.preferences file.
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The key statement in this file is:
["name" => "Local", "installationConfigurationRoot" => "$LS_HOME"]
This line defines both the name and location of the default configuration. In this case, the name of the configuration is Local and it is located in the $LS_HOME , which in the default installation is set to C:\Program Files\SASHome\JMPClinical\12\LifeSciences\ . This is the location shown on the JMP Clinical Settings tab, as shown below:
To add a new configuration, you must copy and modify this key statement so that in defines both the name and the location of where to find the new preference files detailing the configuration.
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Navigate to the JMP Clinical installation folder (normally C:\Program Files\SASHome\JMPClinical\12\LifeSciences ) on your local machine and open the installation.configuration.preferences file with a text editor.
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Copy the key statement, including the square brackets. Enter a comma (" , ") directly after the key statement and then paste the copy directly after the comma. Change the name and location in the pasted copy to the name and location of the configuration. In this case the name is Share and the location is U:\ClinicalShare . Your name and location must be enclosed by the quotation marks. The modified statement should appear as shown below:
["name" => "Local", "installationConfigurationRoot" => "$LS_HOME"],
["name" => "Share", "installationConfigurationRoot" => "U:\ClinicalShare"]
Note : Entries are case-sensitive.
Caution : In the example shown here, the location is specified using a mapped drive path. Locations should contain mapped drive paths only if your organization's setup guarantees that all users have the same mapped drives. If you are unsure, you should use the UNC path instead. If the specified path is just a mapped drive letter (U:, for example), you must include a trailing backslash after the colon ("U:\").
The modified file is shown below:
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Modify the installation.path.preferences file.
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Open and examine the installation.configuration.preferences file that you placed in the specified configuration folder ( U:\ClinicalShare ). All path specifications within this file can be changed to direct metadata and system output to the customized locations of choice.
The key statements that we recommend (at a minimum) changing are highlighted in the image below:
The first key statement is:
{"<userRoot>", "$HOME"}
This line defines the location of the userRoot directory. This defines the top level folder where all JMP Clinical metadata is saved. In this case, the file is located in the $HOME , which in the default installation is set to C:\Program Files\SASHome\JMPClinical\12\LifeSciences\ .
For simplicity, these instructions use the same directory where you have placed the installation.path.preferences for where the new configuration writes metadata.
Note: <userRoot> is used throughout other keys in the installation.path.preferences file . By default this location is also where Templates, Reviews, Notes, and Static Reports along with other related JMP Clinical processing, are placed. This behavior can be changed and managed if desired.
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{"<userRoot>", " U:\ClinicalShare"} .
The second key statement is:
{"/system/clinical/preferences", "$LS_HOME"}
This line defines the location of the system.clinical.preferences file. In this case, the file is located in the $LS_HOME , which in the default installation is set to C:\Program Files\SASHome\JMPClinical\12\LifeSciences\ .
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Change the location in statement to the location of the new configuration at U:\ClinicalShare (or to another location of your choice). Your name and location must be enclosed by the quotation marks. The modified statement should appear as shown below:
{"/system/clinical/preferences", "U:\ClinicalShare"}
The third key statement is:
{"<userLocal>", "$DOCUMENTS\JMPClinical\Local"}
This line defines location where temporary report output while building reviews with JMP Clinical will be. We recommend keeping this location somewhere on the users' local desktops (for example, $DOCUMENTS ).
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{"<userLocal>", "$DOCUMENTS\Share"}
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Save the modified installation.path.preferences file in the configuration location. It should appear as shown below:
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Modify the system.clinical.preferences file (OPTIONAL).
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Open the system.clinical.preferences file using a text editor.
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/*** Role Assignments ***/
{"DefaultRoleAssignment", {"StudyManager", "ReviewAuthor", "Reviewer", "SettingsEditor"}},
{"RoleAssignments", Associative Array({
})}
Note that there are two assignment sections: DefaultRoleAssignment and RoleAssignments . DefaultRoleAssignment lists the roles that all users have by default if no further specifications of user names in the RoleAssignments array are made. RoleAssignments lists each user (using their s User Name) and the roles assigned specifically to that user with regard to the default assignment. Initially, this section is empty by default.
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In the example, shown here, there are three users: userA 1 , userB , and userC . UserA is a Study Manager who can also make and view JMP Clinical reviews; userB is Review Author and Reviewer but does not have Study Management rights; userC is restricted to view finished Reviews only.
Note : For a description of each of the user roles, see system.clinical.preferences , above.
In this scenario the updated DefaultRoleAssignment section could appear as follows:
{"DefaultRoleAssignment", {"ReviewAuthor", "Reviewer", "SettingsEditor"}} ,
Note that roles are enclosed in quotation marks.
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Modify the RoleAssignments section to include each user and their specific roles. In this example, in addition to the default roles, userA is a study manager and userB is a review author and reviewer; userC lacks study manager or review creation capabilities and is a reviewer only.
The updated RoleAssignments section appears as follows:
{"RoleAssignments", Associative Array({
{"userA", {"StudyManager"}},
{"userC", {"-ReviewAuthor"}}
})}
Note that user identifiers and roles are enclosed in quotation marks.
This example used an additive approach to define additional role(s) for userA in reference to the default role assignment. For userC a subtractive approach was used to remove the default "ReviewAuthor" role using " - " in front of the role name; indication the removal of that role from userC . No specification is needed for userB because they match the default role assignments.
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Changing JMP Clinical Configurations
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Click the Settings tab and then on the Configuration drop-down menu. The new Share configuration is now shown as an option.
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Select Share . You must close and reopen JMP Clinical before the new selection takes effect. If the new Share folder is an existing shared folder, studies contained within the folder are displayed on the Studies tab. If this is a new shared folder, JMP Clinical adds the necessary components for the folder to function as a shared studies folder.
Note : Anyone with Read and Write privileges on the shared drive has access to a new shared folder. As the creator of this folder you can control level of access by changing the permissions using WinOS commands.

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Users are identified by the s user name used to log on to the machine and local network.