Configuring Applications Core LIMS Training: Configuring Applications In this tutorial we will discuss how an administrator can make an application. This will help you modify existing applications to better meet your needs or enable you to create your own custom applications. Click on a slide whenever you are ready to move to the next page.

What is an Application? An application is a limited set of related functionality a user might need to use to perform a given process or role An individual user can have one or more applications that they might need to use; they can toggle between any application that is available to them from the Application menu located in the upper right corner of every page Changing applications will automatically change the Application-Specific menus on the left side of the page All applications are pointed at the same database but actions a user is allowed to perform on the data are different Core LIMS provides several applications off the shelf but LIMS administrators can also create their own custom applications What exactly is an application? An application is a set of related functions that a user might need to perform a process or role all put together in a convenient package. You can provide each user with access to as many applications as they need. If they have more than one application, they can always use the Application menu in the upper right corner to switch between applications. An example application menu is shown here on the slide. If you toggle between applications, you will notice the Application-Specific menus across the top left of the page will change. There may also be different dashboard pages that you see when switching to a new application. Each application is using the same database records, but the menus that contain the actions that you perform on records is defined by the application. For example, a sample registration application would give you menus to create new sample records and an inventory management application would give you menus to search for containers or create locations. You will have some applications provided by Core LIMS out of the box. You can modify these or even create your own custom ones. CONFIDENTIAL

Finding Current Applications 1) Navigate to the Main Admin Panel 2) Navigate to the Application Entity Type List You can view what current applications are in your system from the Main Admin Panel. You can use the shortcut in your User Menu to navigate quickly to the main Core Administration page in the Main Admin Panel. Here you can see that Application is a just another Super Type category in the LIMS. You can also list all the Entity Types beneath the Application Super Type. CONFIDENTIAL

List All Applications Select List All to see the current applications Core standard applications will have a ci_app_ prefix in the name; click on the hyperlink to see the record Underneath the Application Super Type, typically there will be the Application Entity Type and the Core Application Entity Type. All the applications provided to you from Core will be stored under the Core Application Entity Type. Click on the List All hyperlink next to this Entity Type to view them. Each application will have a record that is returned as a row in the Smart Table. Core informatics will use a ci underscore as a naming convention so you can easily identify canned applications. You can click on a name or barcode hyperlink if you want to view a single application record in more detail. CONFIDENTIAL

Configuring Custom Applications LIMS Administrators can create their own applications for users for greater control over what a user will specifically see Only expose required functionality Simplifies user navigation Another method to control user access Admins can configure: Icons Java menus Details page hyperlinks User access Dashboard pages As a LIMS Administrator, you can modify an existing application or create your own custom applications from scratch. It is useful to create custom applications for any large group of users that only needs access to a specific set of menus or dashboards. This will make their user experience less confusing by only giving them access to the menus and reports that they need to perform their roles. It will also make it easier for you to support their questions when it is clearer how they need to navigate. CONFIDENTIAL

Steps to Build a Custom Application Create a New Application Give Your Account Access To Application Create Main Menu and Menu Items (Add Super Types and Entity Types) Modify Sub-Menu Functions or Hyperlinks (optional) Create an Application Dashboard with Gadgets (optional) Provide Users Access to Application This slide shows the basic workflow that you will need to go through to build a custom application from scratch. You start by creating a new application record. Then you will need to grant yourself permission to view the application record you created. Next, you can add super types and entity types to the application to create the main menus and submenus. If they haven’t been previously defined in other applications, you can define the sub-menu functions and hyperlinks. You may also want to create a dashboard as a home page for your application. (although that will be covered in a separate tutorial). Once the application has been built to your satisfaction, you can give other users access to the test application. After the application has been tested by your users, you can copy the application from your test system to your production system. Migrate Application From Dev to Production System CONFIDENTIAL

Create a New Application Navigate to Main Admin Panel > Application > Core Application > New Enter the general metadata for the application Tip: The word “Application” will appear in the welcome message so you should avoid using “Application” in the display name To create a new custom application, you just need to create a new application record. If you want your application to be stored with the other applications in the system, click on the New hyperlink next to the Core Application type in the Main Admin Panel. If you prefer, you can also create your custom applications under a separate application type. The Name Display attribute will be the name that is shown in the pull down application menu in the upper right corner. You will add Entity Types to the application later. The other attributes are optional and you can leave them blank. CONFIDENTIAL

Grant Yourself Application Access Use the User menu in the upper left corner to navigate to your Employee Details page Edit the record and add your application to make it available in your Application menu After clicking the Create New button, you will create the application record, but will probably see an error message referring to the fact that you do not have access to view the new record. You will need to navigate to your user record and add the new application to the list of applications that you can view. Hold down the control key to select multiple applications. Click on the Update Employee button to save your changes. CONFIDENTIAL

Application Home Page In a blank application there are no Application-specific menus yet Users without administrative privileges will only see the Welcome message; You can create dashboard pages Will allow you to build the application content Now you will be able to view your newly created application record. Use the application menu in the upper right corner to select the new application. At this point, there will be no menus or dashboard pages yet. You can use the hyperlinks on the page to start developing the menus. CONFIDENTIAL Will allow you to edit the metadata you just entered

Create Main Menus Navigate to your Application Home Page Select Edit Navigation hyperlink Select a Super Type that a user would need access to in the application and select the Edit button The Edit Navigation for this Application hyperlink will allow you to build the main application menus along the top left of the application. Under the Select a Super Type to Edit pull down menu, choose a super type that you want to give users access to and select the Edit button. CONFIDENTIAL

Create Main Menu Items Any previously saved Entity Types will be displayed on the left Remove the number and leave a blank text box to delete the current menu item If there are no Entity Type menu items with numbers on either the left or the right, then the Super Type menu will be removed Available Entity Types that you can add as a menu item are on the right side Type in a number for any Entity Type you want to display as a menu item Menu items will be displayed in numerical order On the right hand side of the page, all the available Entity types are listed. Type in a number for any entity type that you want to add to a submenu underneath the super type you have chosen as the main menu. The entity type menus will be displayed in the numerical order that you enter in the text boxes. The menus in your application will be instantly updated as soon as you hit the Submit button. If you return to this page later, any entity types that are currently added to the application will be displayed on the left. You can remove a menu item by removing the number in the order box and submitting the change. If there are no entity types for a given super type, the super type menu will also disappear. CONFIDENTIAL Click Submit to save changes

Order Main Menus New menus will be created here After you have selected some Super Types and underlying Entity Types, the Super Types will be listed in the Existing Super Types section Edit the numbers on the right to select an order to display the main menus and select Reorder to save changes To edit or remove Entity Types or Super Types use the Edit button Special Cases: Sample-lots will automatically be under Sample menus Report Formats (Entity under List Super Type) will get its own menu If you want to reorder the main menus in the application, you can type in new numbers in the Existing Super Types section and click on the Reorder button to refresh your application menus. The LIMS will automatically assign any new or updated super types that you add to be first in the sorting order, so it is a good idea to finish adding all your entity types first before defining their order. If you have two super types with the same sort number, you will not get an error, but the LIMS will decide which menu goes first for you. There are 2 special cases where main menus do NOT follow the pattern where super type is the head menu and entity types are the submenus. Because Samples and Lots are intimately linked, they are listed together under the Samples main menu with a section for sample functions and a section for lot functions grouped together. Report formats are also listed as a main menu item even though they are not a Super Type just to make it easier for end users to find them. CONFIDENTIAL

Sub-Menu Functions Functions in the sub-menus are automatically inherited from previously set up applications However, administrators can reconfigure them: Navigate to the Main Admin panel > Select List All Entity Types on the desired Super Type> Select Navigation on the desired Entity Type The lowest level of function menus are defined on the entity types in the Main Admin Panel. These menus will be the same no matter which application you are in so these menus can NOT be set separately for each application. If these menus have not already been defined previously or if you want to modify them, you can define them by navigating to the desired entity type in the Main Admin Panel. Select the Navigation hyperlink by the entity type. CONFIDENTIAL

Editing Sub-Menu Functions Just like menu item selections, current sub-menu functions are on the left and available ones are on the right Type a number next to any function you want to display Functions will be displayed in numerical order Leave text boxes blank to remove them Scroll to the very bottom Submit button to save changes Can copy these changes to other Entities of the same Super Type Changes will apply to ALL applications that use these Entity Types Just like the menu item selections interface, you will find the current sub-menu functions on the left side of the page and the available sub-menu functions that you can add on the right side of the page. To add a menu from the right side, just type in a number in the order box next to the menu function you want to add. The LIMS will display the menus in numerical order after you save the changes. If you have two items with the same number, the LIMS will pick the order for you. Note that the LIMS will permit you to add any type of menu but the menu may not work if it is not relevant to the entity type you are adding it to. For example, a lot level report will not work on a sample level entity type. To remove a menu, just remove the number from the Order box on the left. You can also reorder the menus by changing the numbers in the Order boxes. When you are done making changes, scroll to the bottom of the page to save the changes. Note that these menu changes will apply to ALL applications that display menus for this entity type. You can not specify different function menus for different applications. To save you time, you can also apply the same function menus for other similar entity types. CONFIDENTIAL

Details Page Hyperlinks Similarly, the functions or reports that are hyperlinked off a record (Details Page) have already been configured with a default setting, but an administrator can edit those In addition to choosing the function menus on an entity type, you can also choose what hyperlinks are displayed on the details page for an entity type. These are the hyperlinks that are displayed directly below the barcode. CONFIDENTIAL

Modifying Details Page Hyperlinks Navigate back to the Navigation hyperlink of the Entity you want to edit: Navigate to the Main Admin panel > Select List All Entity Types on the desired Super Type> Select Navigation on the desired Entity Type Scroll down to the Functions section You can also modify the hyperlinks from the same page as the function menus. Navigate to the entity type you want to edit the hyperlinks for in the Main Admin Panel. Choose the Navigation hyperlink by the entity type to return to the same page. Instead of modifying the top table you used to modify the menus, scroll down to the middle section where the hyperlinks are defined. You can modify the existing hyperlinks displayed on the left in the same way as you modified the menus. CONFIDENTIAL Make changes exactly like the Sub-Menu Functions

Giving Users Access (List Functions) List All Employees and send desired users to Employee List Function page Don’t forget to include current applications or you will write over them Once you are finished defining your application and you are ready for end users to test it, you will need to give them access to view the new application. You can edit each user record the same way that you did your own, but it is probably more efficient to add multiple users at a time. If you List all the Employees using the List All Menu under the Employees main menu, you can select the users you want to update and forward them to the Employee List Functions page. Choose the new application in the Associate List Members to Applications option. Note that if you select just the new application you just created, it will replace any current applications they have access to. You will want to also select all the current applications they have as well as the new application. You can use the Control Key to multi-select more than one application. You may need to group your users into smaller lists that have the same set of current applications so you do not accidentally change their current permissions beyond adding the new application. CONFIDENTIAL

Giving Users Access (Load Entities) Use the Load Entities tool on Employee to batch update the new application to many users at the same time Separate multiple applications by commas Don’t forget to include their current applications or you will write over them An alternative way to give many users application access is to enter all the desired permissions in a spreadsheet and use the Load Entities tool to update the employee records. Use a comma to separate multiple applications. Again, you will want to include the names of current applications as well as the new one so your users do not lose the current access they have. CONFIDENTIAL

Migrating Applications Once your application has everything you want, you can export an XML file from the application home page to move a copy to another system (like from Test to Prod) The final step after users have tested the application is to copy the configurations from your test system to your production system. On the home page of the application you created, admins will have 2 hyperlinks to export the application to an XML file. The more comprehensive export is one marked full. When you click on this link you will download an XML file that describes the super types , entity types, and the attributes & associations on those entity types that you added as menu items for this application. You can import that XML file into the production system using the application import hyperlink on the Main Admin Panel page.   This concludes this brief tutorial about how to configure applications in the LIMS. Be sure to see the documentation or other tutorials for further information. Import your new application into the Main Admin Panel CONFIDENTIAL