With Clarity LIMS v6.3 or later, there are two ways to search for items:
Basic Search —Searches the entire system or within a specific category, like samples, projects, containers, and protocol steps.
Advanced Search —Locates information stored in the system using specific criteria that cannot be defined in Basic Search.
The Advanced Search function is included in Clarity LIMS v6.1 or later. Advanced Search allows you to search for specific criteria and create relationships that are used to locate information stored in the system. You can use Advanced Search to build detailed search strings (including grouped and nested strings). These search strings provide the search engine with precise instructions on what to look for in the system.
You can use the search toolbar to select Advanced Search from the drop-down list. This selection takes you to the Advanced Search page. You can also access the Advanced Search page directly at /clarity/advanced-search.
Users with Read-Only permissions cannot perform a search using Advanced Search. If a user with Read-Only permissions must use Advanced Search, enable access as follows.
Locate the file on the server (/opt/gls/clarity/tomcat/current/lib/activity-management-ui-config.groovy). Create a backup of the file before proceeding.
Open the file and add the following code:
// To grant Advanced-search access to Readonly user
readonly.allowUrlMap = [
[post: ['/clarity/api/advanced-search']]
]
Restart Clarity LIMS.
From the query builder panel, select a category from the Search drop-down list.
Select Add to add one or more search conditions to the selected category.
If a search condition has other conditions following it, an AND/OR operator is displayed. A search condition contains the following components:
Constraining Entity
Field
Constraint
Constraint Value
To remove a condition, select Delete (X) to the right of the condition.
Use grouping controls to group search conditions by selecting the Show Grouping Controls checkbox. When these controls are enabled, select the checkboxes next to the conditions, and then select Group to group them together. The conditions and groups must be adjacent to each other.
The Query Preview field uses the numbers of each condition to display your search string. To separate the conditions, select the checkbox within the group, then select Ungroup.
The Undo and Redo operations record the state of a search string when you perform one of the following operations:
Add
Delete
Group
Ungroup
Clear all groups
When you select Undo, the string returns to the state before the last operation. When you select Redo, the string reverts to the state after the Undo operation.
After you perform a search, a table shows the results. This table displays the first 500 returning results by default. Use the Configuration Property tool or #applications-propertiesto change the default display.
To export the search results, select Export (down arrow) to the right of the table. Filters applied to the table are not preserved in the exported search results.
You can use the Show/Hide Columns panel to modify columns display in the result table as follows.
Select Show/Hide Columns.
Select the columns for display.
Select Select All to select all columns.
or
Select Clear to unselect all columns.
Select X to cancel any changes made to the selected columns.
Select ✅ to apply the selected columns to the result table.
NOTE: Column filters applied to the result table are preserved when a saved query is created.
The Save Query operation is enabled after a search is completed using a search string. You can use the Save Query panel to save search strings as follows.
Select Save Query.
Enter a descriptive name for the search string.
Select Save.
The new search query shows in the Save Query panel and can be used in future searches.
To view a saved query, select the query from the Saved Query panel. The Query Builder panel shows the conditions and details of the selected search query.
To modify the search query, select the applicable conditions and edit them. When you update a saved query, an EDITED label displays to the left of the query name.
To delete a saved query, select Delete (trash bin) to the left of the query.
To share a saved query, select Share (right arrow) next to the applicable query in the Saved Query panel.
A text file is downloaded that contains the selected query details.
Import a saved search query as follows.
Select Import Query.
Browse for the text file and select Open.
The query builder panel shows the details of the imported search query.
After performing a search with the imported query, select Save Query.
Enter a descriptive name for the search query.
Select Save.
The imported search query shows in the Saved Query panel and can be reused in future searches.
Basic Search is used to search the entire system or search within the following categories:
Samples
Projects
Containers
Protocol steps
NOTE: With Clarity LIMS v6.1 or later, Basic Search will includes more fields of the search category records during a search. We recommend you to use Advanced Search for a more granular search capacity.
Type a complete keyword or search term, or part of the term followed by an asterisk. Search terms are case-sensitive.
The results include all samples, containers, projects, and protocol steps that contain the search term.
Select Search.
In the drop-down Search category list, select All. Type a search term into the adjacent field and press the Enter key.
At the left of the Search results windows, the Category Results panel summarizes the search results and groups them by category.
In the Search results list, the following actions are available:
Hover over the information icon to view more information.
Select on links to drill down further into the data.
When searching for a particular sample, you may want to:
View a list of all steps that have been performed on a specific sample.
See which in-progress steps involve a specific sample.
Determine which steps used a particular derived sample.
When searching for samples, type the keyword or term to search for into the Search box.
Search on the following information, as it relates to a sample:
Select Search.
In the drop-down Search category list, select Sample. Type a search term into the adjacent field and press the Enter key.
You can type the complete keyword or part of the keyword followed by an asterisk.
For example, the search can be performed on the complete sample name (eg, heart-123). However, a keyword followed by an asterisk (eg, heart*) could also be used. The results return all samples whose name include the keyword.
From the sample Search results list, view more information about the sample, including all steps in which it is involved and/or queued.
These options differ depending on whether the sample is a submitted sample or a derived sample.
In QC protocols, you cannot go directly to the queue for a specific step, because all steps share a queue.
Repeated steps display in the sample details search results.
For example, in the previous illustration, suppose that the sample was requeued for the Qubit QC step and the step was repeated. The next time a sample is searched, the step is listed twice.
Searching within the Project category allows you to drill down and quickly find the following project details:
The account and client associated with a specific project.
The number of samples included in a project.
The current project status. For example, at what stage in the workflow samples are currently located and what has been completed.
Select Search.
In the drop-down Search category list, select Project. In the adjacent field, type the project name and then press the Enter key.
Type the complete project name or part of it followed by an asterisk.
From the Search results list, view more information about the project.
For example, the following search results show that the Liver Study project was started on January 27, 2017 and contains 98 samples. The account and client associated with the project are also shown.
Expanding the sample details shows a list of all the steps in which the project samples are actively involved.
In QC protocols, users cannot go directly to the queue for a specific step, because all steps share a queue.
Search within the Container category to search for a specific container by name (Clarity LIMS ID) or quickly find all containers of a certain type in the lab. From the search results returned, the following information can be determined:
Which samples are in the container(s).
Which projects are associated with the sample(s) in the container(s).
What was the last step performed on the sample(s) and who performed it.
Select Search.
In the drop-down Search category list, select Container. In the adjacent field, type the container name and then press the Enter key.
Type the complete container name/Clarity LIMS ID or part of the name followed by an asterisk.
From the search results list, you can view more information about the container and the sample(s) it contains.
For example, the following search results show numerous details:
Clarity LIMS ID 27-301 belongs to a 96 well plate.
The plate contains six samples from the Liver Study project.
These samples are currently in the queue for the Cluster Generation step.
Restrict a search to protocol steps to determine how many steps of a particular type are currently in progress or completed.
Select Search.
In the drop-down Search category list, select Protocol Step. In the adjacent text box, type the step name and press the Enter key.
You can type the complete step name or part of it followed by an asterisk.
The search results list provides at-a-glance information, such as the status of each step, the date the step was started, the user who ran the step, and the number of samples contained within the step.
Various options for drilling down further into the data are provided.
Select Search.
In the drop-down Search category list, select Protocol Step. In the adjacent field, type all or part of the user name to search for and press the Enter key.
The Search results returned will list all of the in-progress and completed steps associated with the user.
Return a sample to the queue for a particular step, so that the step can be repeated or requeued (For details, see ).
| Search Keyword | Applies To | Notes |
|---|
Sample name | Derived and submitted samples |
Derived sample custom fields | Derived samples |
Submitted sample custom fields | Derived and submitted samples |
Container information, container custom fields | Derived and submitted samples | Searchable information includes container name, container type, and well information. |
Project information, project custom fields | Derived and submitted samples | Searchable information includes project name, project owner, and account name. |
Workflow name | Derived and submitted samples | Search on a workflow name to find the samples included in that workflow. |
