A Site is a geographical grouping of Trials.
sites are metadata for contacts and genotypes. A contact’s site may be their employer. Genotype sites are intended to store the origin of a genotype.
An initial Katmandoo installation only includes one site, called Unknown site.
Searching for a site
Searching the database for site records requires 3 fields. A column, a condition, and values. Clicking the search button will build the query based on the selected fields and will produce a table of results below the search box.
Quick Tip: To perform a quick search for all site records, simply click the search button after the page loads. This will run the search using the “All” condition.
To perform a filtered search, select a column to filter using the Column Name drop down.
After a column has been selected, select a filter condition to apply to the column. The filtering conditions available in the drop down are based on the based on the data type of the selected column name option.
Search Field Data Types
String – Alpha Numeric
Decimal or Integer
Changing the condition to “All” will clear any values entered for that rule.
With a Column Name and a Condition selected values to search by need to also be added
The Value(s) text box allows any characters for input.
It also allows multiple line separated values. Entering multiple values will search by each line and apply the “Or” operand to the filter.
To refine the search further, additional search rules can be added using the “Add Rule” button. This button adds an additional filter row to the search input area with the same selections as the previous row.
Additional filter rows provide “And/Or” operands to separate filters. The order of operands may have an impact on the resulting data set.
Additional filter rules can be removed using the “Remove Rule” button. To reset the form click the “Clear Form” button.
After a valid search has been completed, a table of results will be displayed below the search box. To sort and apply paged results additional search controls are available below the filters.
For a default the table only shows 10 Results per page. This can be adjusted by changing the dropdown and choosing a new value
The table will also be displayed with pagination (split into multiple pages). To navigate between the pages there are three buttons that allow to move between pages.
Hitting the “First” Button will go to the first Page while the “Next” and “Prev” buttons will go to the next and previous page sequentially.
The page number of the page being displayed will be shown on the right of the table, just above it. And the amount of results for the search made will appear on the left of the Table also just above it.
The table also gives the option to change how it is sorted. If the “Sort By” dropdown is selected it allows the choosing of one of the Column Names to search by. After the desired Column Name to search by is selected the order (Ascending or Descending) will also need to be specified.
This is set to Ascending by default as represented by the “Down Arrow”. Selecting this Arrow button will change the arrows direction while also changing the order.
The table will not update until the search button is hit again.
Table Controls and Manipulation
Katmandoo also has several tools at a user’s disposal to use to alter and manipulate the results table for a better viewing experience.
Most notably there are five buttons above the table, each with their own function
|This button will immediately export the data in the table to a spreadsheet with the .xlsx for-mat. It is not as powerful as the proper Export but can be useful for checking data quickly|
|This button will immediately export the data in the table to a spreadsheet with the .csv |
format. It is not as powerful as the proper Export but can be useful for checking data quickly
|This button will reset any changes that have been made to the table through the use of |
|This button will copy the table that is shown to the user and put it in the Clipboard (It will |
not copy the whole table, only what is displayed)
|This button will open a small menu of other buttons, each one being one of the column |
|Clicking on any of the headers in this sub menu will either hide or show that column |
(Depending on whether it is currently hidden or showing)
There is also another feature that is not shown with the buttons. That is the ability to reorder the columns based on user preference.
If the mouse is hovered over one of the column headers, there will be a slight colour change. If the mouse is pressed when this happens the system will allow the column selected to be clicked and dragged to wherever.
Adding a site
In Katmandoo 3 there are two ways of adding a site, through Importing and through the search page.
While on the search page, there is an add button in the top right, selecting this button will take the system to the Add page.
While on the site add page, by default there will only be one field to enter data into, site Name.
However if there has been a factor (or multiple factors) created for sites, then there will be multiple fields to enter data into.
After the site Name is supplied, hitting Save will add it to the database
If it was successfully added to the database the system will redirect to the View page for that site
Editing a site
To make a change to a site in the database it must be done through the Edit Page.
To get to a site’s edit page it must first be found in the database. Using the search methods above the site will appear in the results table on the search page.
On the rightmost column of the site there is an “eye” icon. Clicking this will take the system to the view page for that site.
On this view page, there are two options; Back, which goes back to the search page.
Edit which goes to the edit page for the current site.
The edit page looks similar to the add page, but with the addition of the site Id.
To make an edit to that particular site, alter the fields and hit save
If the database was successfully updated the system will return back to the view page for that site and the changes that were just made should be visible.
In Katmandoo there is the ability to add multiple sites all at once by importing data.
The system will only take a file with the type; .CSV or .XLXS/XLS anything else will be rejected.
To begin an import there are two points of entry. There is a global button on all pages on the left in the sidebar. Expanding out sites will give the option to import sites.
There is also a button that allows for importing sites on the search page.
The import page for site will have two different ways for selecting the file to use for the import.
The first option, “Select Import File” gives the option to select a file from any of the previously uploaded files to the system.
If running an import for the first time, this should be empty. However if there are too many files, there is also a “Clear Button”
The other option allows files to be directly uploaded from the device Katmandoo is currently being accessed on.
On the import page there is also a button that will automatically generate a template XLXS file that has all the possible headers for sites.
The template has two sheets with the first one where the headers are located and where data would be inserted. The second sheet merely has all the information surrounding the headers and any factors.
If an XLS or XLXS file is uploaded the system will come with another prompt if the spreadsheet has more than one sheet.
Once a sheet is selected and the “next” button is pressed the system will show all of the headers from the file and try to automatically map them to Columns in the Database.
If a CSV file is uploaded or if an XLSX /XLS with only one sheet in the spreadsheet, the system will skip the prompt for choosing the worksheet and will show the headers with their relevant mapping.
The system will try to match the column headers to the database fields automatically, but if it didn’t there it can be done manually.
If there are any headers that need to be uploaded that are red and have a cross next to them, it means that they are not mapped to a database field and need to be set manually.
By clicking on the dropdown that says “–Not Mapped–“ the system will show all of the database fields that are linked to site Table in the factors (columns). It also includes all the aliases of them as well.
The system will also show at the top of the page how many columns are mapped out of how many can be mapped.
As well as letting the user know which columns are needed for mapping and if they made any of these duplicates
If all of the required fields have been mapped to databases and the next button is hit, the system will come up with confirmation.
If there are new records in the data base the system will number the amount of new records it will be adding.
If records a just being updated then the system will give the number of records being updated also.
After hitting save, the system will attempt to make those changes to the database returning a positive message on the home screen if it was successful.
To confirm that the import was done without error. Go to the Search Page and run a search for the newly imported sites
On the site’s search page there is a button for exporting data.
By clicking the export button a the system will generate a pop-up
The export site Data popup has several buttons and dropdowns with some being more useful than others.
The first dropdown cannot be changed as there is only one Export type for site
Under the heading “Available Columns” there is a full list of all of the available columns for export. Under the export type there is an option to choose an export template which will allow users to save a template of the columns they want form that list to export.
The two default settings are, all columns and no columns.
When doing a data export it can be time consuming having to go through very large lists of available columns.
However Katmandoo allows the creation of templates which can alleviate this issue.
When creating an export template, first the “new” button will have to be selected, in the Export Template Row
After this, a new row will appear asking for the new Template’s name.
To create a template first all the columns that are desired must be brought across from the available columns list. Then while in the Export Columns list, they can be ordered by using the up and down arrows.
If a name is supplied and the desired columns are added then hitting the save button will Save the template.
Then if the template is to be used, it will now appear in the dropdown
Going into any export and then hitting apply will automatically add what was save in the template (If it exists in the Available columns list).
To choose what columns are needed the blue buttons in the middle are used for this navigation.
Please note that by holding in shift multiple Columns can be selected at a time
|This button moves the selected available column to the list of Export Columns|
|This button will move all of the available columns to the |
Please note that for large amounts of columns the system
may take time to load
|This button moves the Export Columns out of the list of |
|This button will move all of the export columns back to |
the list of available columns
|This button will move all of the selected columns up in |
|This button will move all of the selected columns down |
in their order
Another feature that exits for ease-of-use in the export window is the two search bars
There is also an option at the bottom of the window that is prompting for a file format to export to.
If there are large amounts of columns in either the available columns or the export columns lists. There is the ability to search for something specific.
The list will filter as characters are entered and if there is no possible match it will appear blank.
There is also an option at the bottom of the window that is prompting for a file format to export to.
By default this is set to be a CSV file, but it can be changed to be a XLSX file.
Once a set of Export columns are selected, hitting the “Export” button will allow the system to download the exported file.