1. Report Formats, Lists, and Custom Reports
Core LIMS Training:
Report Formats, Lists, and Custom Reports
Welcome to Core LIMS Training. In the last section (Canned Reports & Queries), we learned about the reports that come with the LIMS out of the box. This chapter will cover how we can start to build our own custom reports. We will demonstrate report formats, which are used to define what data fields you want to return, lists, which are used to define sets of records, and reports, which are used to store and re-run your query criteria.

2. Course Topics Creating a new report format
Editing a finished report format
Applying the report format to a set of compounds
Applying the report format to a query
Creating Lists
Create Report menu
Storing Queries as Reports
Live Reports
Scheduled Reports
This chapter will begin with a demonstration of how to create a new report format. We will then demonstrate how a report format can be modified once it has been built. Next we will learn how to apply the report format to a set of compounds or to a query. This chapter will then demonstrate how to create and use LISTS to store sets of records. We will look at how we can combine report formats and lists to create a simple report with the Create Report menu option. Finally, we will look at how we can store query filter criteria in Report records so that we can re-run those queries later (either on demand or run at scheduled times).
CONFIDENTIAL

3. What is a Report Format?
Way to define what data columns go into a Smart table
Can be applied across any list of samples to make your own custom report
Can be created by a LIMS administrator or almost any end user
Public or private
Can contain data columns from any Entity type
Most common report formats allows columns from sample, lot, and assay entity types
Other report formats only allow you to select the attributes on that entity type or attributes on entity types that are associated to that entity type
In the prior lesson we looked at the Canned Reports that are provided by CORE LIMS out of the box, and saw the variety of report options that are already provided. However, what if you want to choose your own columns to report on and define your own customized report? This lesson will demonstrate how that can be done. The Report Format capabilities allow the user to define the exact data columns they would like to see in a table. Later, this set of data columns can be applied to any set of records, or essentially table rows, that you want.
Report Formats are not limited to just LIMS administrators. Generally, most users have permissions to make them. Report formats can either be public and shared by many users so that everyone can have the same view or they can be private so that you can make your own personal report formats.
In most cases, users are working with an Assay Report Format. This type will allow you to pull any combination of columns from sample and lot attributes as well as any type of assay data.
You can also create report formats for other entity types in the LIMS. However, for these you can only pull columns for the attributes on that entity type or any associated entity type for reporting.
Lets move on to see exactly how Report Formatting can help to create customized reports.
CONFIDENTIAL

4. How to Make a Report Format
Create Report Format allows you to define a new list of columns
List All allows you to find (and potentially edit) Report Formats that are previously defined
The first step in creating a customized report is to create the report format. This will define the columns you wish to see on your report.
There are 2 ways to create report formats – you can either create them from scratch or you may create them automatically from a query. Let’s start by showing how to create one from scratch.
To create a Report Format from scratch, we need to navigate to the Create Report Format page. There is usually more than one way to get there. You can often navigate from a Create Report Format menu. This menu option can be under a List or a Report Format main menu. It is also possible to see this menu under a sample entity type or other entity type. Let’s navigate from the Report Format main menu this time.
Typically, there are two options on the Report Format Drop Down list.
The List All option will provide you with a list of all previously defined Report Formats, allowing you to make edits to them if needed.
The Create Report Format option will allow you to define a new list of data columns to be used for future reports.
CONFIDENTIAL

5. Create a New Report Format
Type in a descriptive name that will be easily recognizable in a pull-down menu
Assay Entity Type will also allow Sample and Sample-Lot fields; other Entity Types will just provide fields within that Entity Type and any fields associated to that Entity
If you check the box, only you can see this report in Core. If you do not check it, you can share the report format with other on your team, but sharing too many reports will make a long pull-down menu for everyone.
Select a project and hit the Create New button
After clicking on the Create New Format option from the drop down list, you will be taken to the Create New Report Format page. This will allow you to create your new report format.
First, enter a Name. Type in a descriptive name that will be easily recognizable when displayed in a pull down menu so that users will know which report format to select.
Depending on how you navigated to this page, you may be asked to select the Entity Type. In most cases, you will want to select the Assay Entity Type. The Assay Entity type will allow you to select both Sample and Sample Lot and assay data fields together. Note that will not be able to include container or data fields from other entity types with this type of report.
If any other entity type is chosen, then the only those fields within that entity type can be used, along with any fields associated to that Entity Type.
Checking the Private box will allow only the creator of the Report Format to see the report format in CORE LIMS. If this is unchecked, then everyone will have this Report Format available in their pull down menus. Keep in mind, that while its nice to have many option available to the user, sharing too many report formats will make for very long pull-down menu for everyone to have to look through.
The Projects field is next. Select a project and then click on the Create New button to create your Report Format.
CONFIDENTIAL

6. Report Format Record
Click on the Add/Remove Members link to start defining the columns you want to put in your reports
This will bring you to the List Details Page. This page will display all of the details of your newly created Report Format. Upon creating the new Report Format, CORE LIMS automatically creates a database view in the Core LIMS Schema. Other applications can point to this view if desired. This is a great way to integrate external reporting tools to get more value from the data in your LIMS.
To add or remove columns from this Report Format, simply click on the Add/Remove Members link located under the Action Toolbar.
Report Formats automatically create a database view in the schema that other applications can point to
CONFIDENTIAL

7. Choosing Sample or Lot Columns
3. Click Update List to save the new column(s) to your report
2. If you want to re-name a column, type the desired name in Alias field (if multiple columns selected, all will get the Alias name)
1. Select 1 or more columns from the pull-down menus. (Use Shift or Control keys to multi-select)
Clicking on the Add/Remove Members link will bring you to the Report Format Members Details Page. This page will allow you to select those columns for the report. The Sample Data section will allow you to add Sample columns, the Lot Data section will allow you to add Lot columns.
Hold down the shift or ctrl key if you are selecting multiple fields.
Click on the Update List button to add those fields to the report format.
Once the fields have been selected, the current fields will be visible at the top of the page and you can still select more at the bottom of the page.
Now there is an Alias column that will allow you to rename the display name of the column header in the report. This allows you to make the columns read more user-friendly on the report.
Select Update List button again to save any Alias values you add.
CONFIDENTIAL

8. Choosing Assay Report Columns
1. Select Assay Type to populate other menus
3. Select any other options:
Sample Centric - average different lots with same conditions
Grouping – if the assay has pre-defined sets of groups (like different concentrations tested) you can pick one to add to report
Protocol – you can specify compounds that follow a specific protocol be reported
Aggregate Function – you can get other statistics besides an average (add 1 row at a time to get multiple statistics in report)
User Defined Equation – you can perform math operations on a database column
Assay Report columns can be selected in addition to sample and lot information. First, select the Assay Type. This will populate the other menu options going forward.
Next, select the Assay and Data Types desired for the report. Once you click on the Update List button to add columns to your report, you may also want to rename your column headers using the Alias column, just like for sample and lot columns.
Finally, there a few more options available on the page that give you some different ways to aggregate or process the data. These are detailed in the documentation.
Once all of the updates are complete, click on the Update List button again, to save any new changes.
CONFIDENTIAL
2. Select Assay and Data Types

9. Modifying The Report
To reorder the columns in your table, click on the Sort Members link
Edit the Alias field if you want to rename any columns
Select the Remove box if you want to delete unwanted columns later
Our existing report format can be modified at any time, once it is created. Columns can be removed by simply clicking on the appropriate remove check box and clicking on the Update List button. Additional columns and Alias values can be added at any time and updated.
Clicking on the Sort Members link will open the Sort Report Format Members page.
CONFIDENTIAL
Continue to add more columns as desired (one at a time)

10. Sorting Report Columns
1. Type in desired sort order
2. Click Save Sort Order to save new order
The Sort Report Format Members Page will allow you to set the sequence of the columns as you would like them to be ordered in the report. Simply set the desired sort order and then click on Save Sort Order to save your changes. Note that users can always reorder the columns on the fly in the Smart table, but this page sets the default column order.
CONFIDENTIAL

11. Editing a Report Format Later
Edit Icon can be used to deactivate the record if you want to remove it from view. It does NOT edit the columns in the report.
Go to Report Formats > List All to find your record
Click on Add/Remove Members to add or remove or rename columns
Once your Report Format has been completed, you have the ability to DeActivate the Report, so it is longer available as a Report Option in pull down menus. Locate your Report Format record from the Report Formats  List All menu option. After locating your record, click on the Edit button from within the Action Toolbar Options. The Edit button will allow you to uncheck the “Active” box to deactivate the Report Format. The Edit button will NOT allow you to edit the columns within the report. Remember that can only be done by clicking on the Add/Remove Members link from the specific Report Format page.
CONFIDENTIAL
Go to Sort Members to reorder the columns

12. Applying Your Report Format
Now you can pull the data for the specific columns in your Report Format for any list of compounds using the Generate Report on the List Functions page
Now that the Report Format has been completed, let’s look at the various ways that we can use the Report format to return data.
One way to use the newly created Report Format is to send a group of compounds to a List Functions page and then generate a report that displays the data columns that were stored in the Report Format. In a prior lesson we learned how to populate the List Functions Page, (pasting values, typing them in, using a query), so with the List Functions Page populated with List Members, lets look at how our Report format can display this data being passed into it.
Locate the Generate Report section and in the Report Name field, select the newly created Report Format. You can specify how you want the report to display. The html format will return the interactive Smart table. You can also export the data into Excel or as an SD file if you have chemical structures.
Don’t forget to click the radio button for the Generate Report option, and then click on Submit at either the top or the bottom of the page to get the report.
CONFIDENTIAL

13. Applying Your Report to a Query
You can also apply the same report columns to queries. Set your filter criteria as normal but select Report Format and choose the Report Name you want.
You can also apply the Report Format to a query directly. This is an alternative to returning query results in list format which gives you all attributes of only the returned entity type. So for example, if you were returning lots in list format, you would see all the lot attributes. If you apply a report format to a sample query page, then you can see the sample, lot, and the assay results that are important to you.
As a review from the previous lesson, you can navigate to the Full Sample Query page from the Query Menu. On the Query Search page, select the Report Format option and select your newly created Report Format under the Report Name drop down menu. Note that if you forget to select the Report Format option, your results will probably be returned in List Format even if you select a desired Report Format record.
CONFIDENTIAL

14. Query Can Create a Report Format
You can directly start a new Report Format from a Sample Query page. Select ‘Derived from criteria’ as your Report Name and give a new unique Report Name under Save Report.
Sample or lot filter criteria you set will not automatically be included as a report columns and you can display columns that were not used to filter data. Check the boxes in the Select column on the right to choose columns for a report format.
You can also create an entirely new Report Format directly from this Query Page. Simply set the Report Name to: Derived from criteria and enter a new Report Format Name in the Save Report field.
Set the Query criteria as you typically would. Be aware, however, that the fields you select for the Query criteria do not necessarily have to be the same as the fields that are returned on the resulting report. To determine the fields on the report, check the Select box for that particular field that is desired to display on the report format.
In regards to Assay data, assay filter criteria will automatically be included. If you want to include an assay column, but not filter data by it, then chose the select for report option.
When you run the query, you should get an interactive Smart table with all the rows that passed the filter criteria and the columns that you selected on the Query page. You will also automatically have stored a new private Report Format record in the LIMS that you can re-use later. If you return to the Query Page, you will be able to see your new report format in the pull down menu of report names that you can select from. The name will automatically have a time stamp appended to ensure that the report name is unique, but you can navigate to the report format record (use the List All menu) and edit the name if needed.
Assay filter criteria will automatically be included. If you want to include an assay column, but not filter data by it, choose the Select for report option
This is a great way to quickly start a report, allowing you to edit column ordering or rename columns later if needed.
CONFIDENTIAL

15. Can I Save a Set of Samples?
Yes, you can save any list of samples as a List
These can be public lists shared with everyone OR you can define your own private customized lists
You can start a new list or add to an existing list from the List Functions Page
Once your list is saved, you can quickly apply any report format or task to those compounds
We have discussed how you can save a set of data columns for a report table. Let’s move on to show how you can save a set of rows for a report table. Suppose for example, you have a set of samples returned from a query, and you would like to save them, and apply them to other reports? This is possible by saving the list of samples as a LIST. Just like a report format (which is essentially a list of columns) this LIST of samples can be made public, allowing others to access the list of samples, or it can be made private, so that only the specific user will have access to the list. Once saved, it can then be applied to any report format or task. Let’s take a look at how that can be done.
CONFIDENTIAL

16. Starting a New List
1) Transfer a list from a query or paste a list of compounds into the box on the List Functions page
2) Type in a descriptive name that you can recognize in a pull-down menu
3) If you check the Private box, only you can see this list in Core. If you do not check it, you can share the list with others on your team, but sharing too many lists will make a long pull-down menu for everyone.
4) Select a List Type
5) Select the radio button
6) Click on the Submit button
To create a new LIST, navigate to the List Functions page, populating the List Members section with a group of compounds to search on. Navigate to the List Management Functions section of the list functions page to the Add to New List option. This is where you have the ability to configure the list properties. Set the Name to a descriptive name that you can recognize from a drop down list, set the Type field to LIST, determine if the list is to be public or private, and then select the radio button for the Add to New List Section, and click on submit.
CONFIDENTIAL

17. Viewing Your List
Click on Forward to List Functions to transfer the list for reports or actions
In View Member Details section, you can view or remove compounds
Click on Sort Members to reorder the list
You will be directed to the new List Details record that you just created. Click on the View Member Details link to view the current members of the list. You can remove unwanted members on this page selecting checkboxes in the Remove column. You will NOT be able to add more members to this list from this page – you will need to do that from the List Functions page.
Back on the main List Details page, you can click on the Forward to List Functions link to transfer the list to a report or perform an action. The Sort Members hyperlink will let you set the order of the data that is returned.
CONFIDENTIAL

18. Adding New Compounds to a List
1) Like before, transfer a list from a query or paste a list of compounds into the box on the List Functions page
2) Select from previously saved lists
3) Click on the radio button
4) Click on the Submit button
With the LIST now created, it may be that some time down the road, you may want to add additional compounds to the exiting list. This can be done by navigating back to the List Functions Page, populating the List Members Section with the compounds that need to be added to the existing LIST.
Locate the Add To List Section, and select the List to add the new compounds to. Select the radio button and click on the Submit button.
CONFIDENTIAL

19. Create Report Menu
A quick way to get up to the minute data on a standing report without going through the List Functions page…
2) Pull-down your pre-saved Report Format
1) Pull-down your pre-saved compound list
Let’s move on to look at one quick way to get up to the minute data on a standing report without having to go through the List Functions Page.
To do this, navigate to the Create Report From List menu option underneath the Samples main menu. You LIMS administrator can configure this menu if you are missing it. This will take you to the Generate Report page.
From the Sample List drop down field, select the desired Sample List you have created previously. From the Report Format option, select the Report Format previously created. Select any of the Reporting Options desired, and click on the Generate Report button.
This will give you a table of your saved lists crossed with your saved columns. This report is useful if you have a set of samples that you following for a specific set of assay results that values will be entered into the LIMS over time. For example, this is a useful way to build a structure activity relationship (or SAR table).
Although you have stored the list and report format records in the LIMS and can quickly regenerate the report on demand by just making 2 pull-down selections, this report is NOT stored in the LIMS as an explicit record.
CONFIDENTIAL
3) Click on the Generate Report button

20. Can I Save a Query?
Yes, you can save the filter criteria for a query as a Report
2 Report Types
Query re-run when report is opened (Live)
Query run on a schedule and cached (Scheduled)
Reports do NOT have a concept of public or private
Anyone who knows a report barcode or name can navigate to it
Any user can simplify access to a report by adding it to favorites folder
Admins can add reports to menus
Admins can put reports in gadgets that are displayed in dashboards
You can however, store a report in the LIMS. Although we loosely use the word “report” to refer to any page that is displaying information, in the LIMS we use the Super Type “Report” to store a query and the query output. Basically, when you enter query filter criteria and possibly even choose a report format output, that information can be stored as a Report record that can be re-used again.
There are two types of reports that can be created from within CORE LIMS. These are categorized as LIVE reports and Scheduled Reports. Live reports will re-run the query whenever you open the report entity. Scheduled reports will run the query on a schedule that you define and will store the results on the report record so that you can quickly look at the cached results. If you need to update the report, you can re-run the query on demand.
One thing that is different from Report Formats and Lists is that Report records do NOT have a concept of private and public. Although any user can create a report, the report is not easily shared with other users unless an administrator adds the report to an application (which will create a menu for it) or the administrator adds the report to a gadget. If a user creates a personal report that they want to return to view often, it is recommended that they “like” the report to add the page to their Favorites folder so they can easily return to it. Any user that knows the barcode or name of that report record can navigate to it and view it using the Quick Find Tool. If there are specific reports that need access to be limited to a specific set of users, then an administrator can implement project-based security.
CONFIDENTIAL

21. Live Reports
Re-runs the stored query any time a user opens the report record
From the Data Table that is returned from the query, Save as Live Report
2) The report can also be associated with an application and then added to the Reports menu option.
1) If the user “likes” the report, it can be run LIVE from the Favorites bar, at any time.
To create either a live or scheduled report, the user needs to start from a query page. Enter whatever filter criteria that you want to search for. If you want to apply a report format to define what data columns are returned, specify that on the query page also. Go ahead and execute your query using one of the Submit buttons.
The query results will be returned in a Smart table. Since the results have come from a query, there will be an extra Save menu within the Smart Table menus. Note that the Save menu will NOT be available if you have navigated to a Smart table from a different way, such as a List All menu. Underneath the Save menu you will be able to select saving the report as a Live or a Scheduled Report.
Selecting the Live Report option will take you to a Create Report page. It is a good idea to enter a descriptive name to help you find the report later. When you create the record, you will be directed to the Report Details page. You will see the data for the report in a table at the top of the page. As you scroll down the record, you will see that the LIMS has automatically written out the JSON query that will be run every time you view the report record. You can edit the record if you want to modify the JSON query later.
As an end user, you may want to click on the Like icon. This will add the report page to your Favorites folder so that you can easily return to the page. For a Live report, the query will automatically run every time you navigate to the page so you will have the most recent data.
If the report needs to be viewed by many users, then an administrator can create a menu item that will make it easy to navigate to this page. To do this, the administrator needs to edit the report record to add an association to an application (or multiple applications) where the report menu will be displayed. Next, the administrator needs to edit the navigation for each application to add the Live Report as a menu item. This was covered in detail in an earlier lesson on Configuring Applications. Once the Live Report entity type is on the application and the application is associated to the Live Report record, the LIMS will automatically create a menu item that users can click on to navigate to the page.
The administrator can also add a report to a gadget so it can be included on a dashboard display. This will be covered in the next lesson.
CONFIDENTIAL

22. Scheduled Reports Allows you to run a report at a scheduled time
Caches results for faster page loading
Can still be run on demand as needed for latest results
From the Data Table that is returned from the query, Save as Scheduled Report
Configure when to schedule the report to run.
You can similarly create a scheduled report. Scheduled reports can be run on a set scheduled time, and the results are cached into memory at the time they are run. The report page can then be quickly opened at a later time since you do not have to wait for the query to complete. It also helps with overall performance by reducing the number of times a large report has to be run if the page is going to be viewed often by many users.
Just like the live report, you will define the filter criteria and select any report formats on the query page. From the Smart table, you will select the Save as Scheduled Report from the Save menu. This will take you to the Create Report page. As with Live Reports, you will want to enter a descriptive name. However, the main difference here is that you will need to associate a scheduled report to a job to define how often the report should be run.
By default, a scheduled report can be scheduled to run daily, hourly, monthly or weekly. If desired, you can create your own custom schedule by simple creating a new Jobs record. Check the documentation for more details.
Just as with Live Reports, when you create the record, you will be directed to the Report Details page. At the top of the page, the report has not been run yet (since it was scheduled for later). There is a Refresh Report button that you can hit to run the report now. While the report is running, the Refresh Report button will not be displayed. You can refresh the page by clicking on the name hyperlink for the record. When the report is complete, you will see the data at the top of the record and the Refresh Report button return.
As you scroll down the record, you will see that the JSON query and farther down you will see details about when the report was last run. If you are not sure how old the data is, you can always check in this section before deciding to click on the Refresh Report button.
Just like for the Live Reports, you can like your Scheduled Reports or an administrator can make a menu item in the same way.
This concludes this chapter on Report Formats, Lists and Custom Reports. If there are any topics that you feel you need to review, please go back and review those topics at this time. If you are comfortable with this lesson, then please move on to the lesson on Gadgets and Dashboards. Thank You!
CONFIDENTIAL