Table of Contents

guest
2021-04-12
Workflow
   Start a New Job
   Manage Job Queue
   Complete Tasks
   Manage Notifications
   Edit Jobs and Tasks
   Manage Users and Permissions
   Create a Job Template
   Manage Jobs and Templates

Workflow


LabKey Sample Manager makes it easy to plan and track your tasks with these lab workflow features:
  • Create jobs to track and prioritize sequential tasks
  • Assign work to the right users
  • Use workflow templates to standardize common task sequences
  • Track progress toward completion

Topics

Tutorial

Get started with workflow in the Sample Manager tutorial step: Tutorial: Outline Workflow.




Start a New Job


Workflow jobs organize related tasks into a sequence of work to be completed. A set of samples to be worked on can be associated with the job, and it can include direct links to upload data for the necessary assay tests performed on those samples.

To start a job, you can either start by selecting the samples you want worked on, or add them to the job later. It's also possible to have jobs that do not involve samples, if that supports your lab workflow.

Start a Job

There are several ways to open the job creation wizard:

  1. From the home page, click Start a New Job.
  2. From the sample or assay dashboard, select Create > Job.
  3. You can also select Jobs > Start a Job from any samples grid.
  4. Select some samples and then use Jobs > Start a Job with Selected Samples.
This final option is described next. If you are creating a job without pre-selecting the samples, skip ahead to the Job Details and Priority section.

Start a Job with Selected Samples

If you already know the set of samples you want to include:

  • Select the sample type of interest from the Sample Types section of the main menu.
  • Use filtering and checkboxes to select the Samples of interest on the samples grid.
  • Select Jobs > Start a Job with Selected Samples from the menu above the grid.
    • Note that if you select Jobs > Start a Job, the new job will not include the selected samples.

Job Details and Priority

On the first panel of the job creation wizard, enter details about the job:

  • Job Name: Provide a name for the job, or leave blank to have one generated for you.
  • Description
  • Job owner: This can be the user who "owns" the overall job completion, or the user to whom you assigned the first task.
  • Notify these users: Add users who should get notifications as this job progresses.
  • Job start and due dates: Use the date picker to select the begin and end dates.
  • Priority level: Use the pulldown menu to select one of the options:
    • Low
    • Medium
    • High
    • Urgent

Define Job Tasks

Click the Define Job Tasks section to open it.

Any job can be composed of several tasks to complete in sequence. For each task in your job, enter the name in the Task column, select any Assays to Perform as part of that task, and use the dropdown to select an Assignee.

Use the six block handle on the left to reorder the tasks.

Each task can also be opened using the (expansion) icon, where you can add a more verbose Task description and use the date picker if you want to assign a Due Date for the task (independent of the due date of the job at large).

Once you have added tasks to a job, the button near the top to Save as Template will be activated. If you want to save the current set of tasks and files as a new named template, click this button. Note that this will exit the job creation editor and a new job will not be created at this time.

Assign Samples

Click the Assign Samples section to open it. If you created this job from a set of samples, it will open on the Included Samples tab and you will see them listed. If not, skip ahead to search for samples

Included Samples

  • Review the listed set of included samples using the omnibox (entry box reading "Select...") to sort and filter, and if necessary select one or more rows and click Remove from Job to remove them.
  • If you like, you can use the Search for Samples tab (described below) to add more samples.
  • When you are satisfied with the selection of samples, click Next and skip to the Attach Files section.

Search for Samples

  • If you did not start creating this job from a selection of samples, when you open the Assign Samples panel, click the Search for Samples tab (if it is not open by default).
  • You can search for names or attributes in the search box. Click Search.
  • Click Show Filters to see a set of selectors for filtering to find the samples you want. Options:
    • Of Sample Type
    • Created by
    • From Parent
    • Date Range From/To
  • Make selections for some or all filters, then click Search. This will populate the search results in a grid below the filter section.
    • Scroll, or use the omnibox to sort and filter to find desired samples.
    • You can also change the Filters above the grid and click Search again if you haven't found what you need.
  • Check the boxes for the samples you want to include. Once samples are selected, the "Add to Job" button will be activated.
  • Click Add to Job.
Now, if you click the Included Samples tab, you will see the samples you added. You can return to Search for Samples again if you need to add more.

Attach Files

Click the Attach Files section to open the final wizard panel. You can drag and drop to upload any files needed for the job. For example, an SOP document or other instructions related to the job could be included here.

Any files you upload will be listed; if you need to delete one, click the to remove it.

Finish Creating Job

Before finishing job creation, consider whether you want to make this job available as a template for creating similar future jobs. Creating a template from a job is offered only during initial job creation.

  • Click Finish Creating Job to start the job without creating a template.
  • Use the dropdown menu option Save as Template and Start Job to create a template and start this job.
You will see the job overview. Note the tabs along the top edge for viewing Tasks, Samples, Assays, and Files in addition to the Overview.

Create Template from Job

As you finish creating a job, you could select either one of two alternate ways to save the job as a template.

  • Save as Template
  • Save as Template and Start Job

Either of these options will turn the task sequence you just created into a template that can be used to create future similar jobs. In a popup, you will name the template and provide an optional description.

Note that you can only create a template during initial job creation - once the job has been started, you cannot generate a template from it.

Learn more about creating job templates in this topic: Create a Job Template

Create Job From Template

You can create a job from a template you have already saved, with or without the preselection of samples. Creating a job from a template follows the same wizard process, but the description, tasks, and other details are preconfigured.

  • At the top of the job creation page, click Choose Job Template.
  • Select the template from the dropdown - typing ahead will narrow the options.
  • Click Choose Template.
A banner message will confirm the selection, and the template tasks and files will be prepopulated in the job wizard. You can click Remove in the banner to remove the template if desired.

Add Job Details and Priority

The template does not prepopulate the Job Details and Priority panel; complete it as when you are creating a job without a template as described above.

Define Job Tasks

The job tasks from the template are prepopulated in the job creation wizard. You can assign these to users.

By default, the task names and assays are read only. If you want to make changes in the tasks, click Edit Tasks and edit using the same interface as when you create tasks without a template.

Complete Wizard

When you are defining a job starting from a template, the sections to Assign Samples and Attach Files are the same as above for creating a job that did not start from a template.

When you have completed all the sections of the job creation wizard, you have the same options for finishing as described above. Your new job created from a template can be used to create a new template, just be sure to give that new template a new name.

Jobs that were created from templates show the template name on the Overview tab of the job details. Click the job name to open the job details, then click the template name to open the template itself.

Related Topics




Manage Job Queue


Once jobs and tasks have been created and assigned to you, you will immediately see your own work queue from the home page in the Jobs List. You can also easily see information about jobs assigned to others.

Jobs List Dashboard Panel

On the home page, the Jobs List shows Your Queue by default. This is the list of jobs that are either assigned to you or include tasks assigned to you. Filter your queue by Priority Level using the dropdown.

You can switch to Active Jobs by clicking the tab, and the view will show jobs assigned to others as well.

Click the name of any job to see the job details and task list.

Jobs Home

Click Jobs Home or select Workflow from the main menu. There are two ways to view the job data.

Job List

By default you see the Job List grid view:

By default, the grid is sorted by due date. Like other grids, you can use filtering, sorting, searches, and custom views on the grid of jobs.

The tabs each show the count of jobs in the different categories:

  • Your Queue: Jobs and tasks assigned to you.
  • All Active Jobs: Jobs that have not been completed, including but not limited to the ones in your own queue.
  • Completed Jobs: Jobs that have been completed.
  • All Jobs: All of the above.
  • Job Templates: See all the active templates.
Click the name of any job or template to see the details and task list.

Administrators have more options for managing jobs, as described in this topic: Manage Jobs and Templates.

Heatmap

You can also view the workflow data as a heatmap. You will see color blocks representing the number of jobs created from each template over the past year. Jobs not created from templates are grouped in the first row. Hover over a block for details, click to see a filtered grid.

My Queue

At any time in the application, you can select My Queue from the workflow section of the main menu to jump to a detailed view of your own work assignments.

Related Topics




Complete Tasks


This topic covers the process of marking tasks and jobs as completed. It is important to note that there is no checking that the work specified in the tasks in question was actually completed in the lab; these tools offer a tracking mechanism for humans completing their work.

Open a job by clicking the job name. Find it:

  • On the Jobs panel on the home dashboard under Your Queue if it is assigned to you. You can filter by priority to find the most pressing work.
  • If the job or current task is not assigned to you, you can click the Active Jobs tab on the home page, or the Jobs Home link for a grid of all jobs.
  • Use the main menu from anywhere in the application. Click Workflow for the grid of all jobs.

Topics

Overview Tab

On the Overview tab, you will see the job details and list of tasks (Job Progress and Assignments) with status of each task. Status values include:

  • In Progress: the current/active task to be completed
  • Pending: future tasks that need to wait for the 'in progress' task
  • Complete: completed tasks.

Tasks Tab

Switch to the Tasks tab to see a more detailed view of job progress. Each task is listed in the Job Progress panel.

Completed tasks show a checked box. Tasks that involve assays include an Import Data button.

Switch among tasks by clicking the task name.

Comments

In this view, you can enter Comments to accompany any task, including the ones marked completed. Use the dropdown to switch among sort orders for existing comments:

  • Recent first (Default)
  • Oldest first
Add your own comments or notes about the step in the box. Click Comment to save.

Complete Task

If the 'In Progress' task is assigned to you, and you have performed the actual work described, you can click Complete Current Task on the Overview tab (or Complete This Task on the Tasks tab) to mark it completed. The task status changes to Complete and the next task on the list is now In Progress.

If the 'In Progress' task is not assigned to you, the button for completing the task will be inactive so that you cannot inadvertently complete others' tasks. Administrators are exempted from this restriction and can both mark any task as completed and reassign tasks as needed.

Complete Tasks with Samples

When your task involves running an assay on a set of samples, you can access and review the samples to be tested on the Samples tab:

Actions available here:

Complete Tasks involving Assay Import

Return to the Tasks tab and click Import Data to open the importer for the requested assay. If multiple assays are associated with the task, the Import Data button will be a dropdown menu so that you can select each assay.

Once the import is complete, you can click here in the green banner to return to the workflow job you came from.

Reassign Task

From the Tasks view, users with sufficient permissions can reassign tasks that have not been completed by changing the Task Owner. Click Reassign after selecting a new task owner.

Reopen Task

If you find you have closed a task by mistake, you can reopen it using the Reactivate Task option on the menu for the task.

Related Topics




Manage Notifications


In-app Notifications

Notifications of interest to each user are shown in a menu in the header bar. If any background imports are in progress, the bell will be replaced with a . The number of waiting notices will be shown in orange, superimposed on the bell or spinner icon.

Click for a listing. Each notification has a corresponding status, time of completion, and link to either the successfully imported data, or to more information about an error.

Email Notifications

Users can control whether they receive email when events occur regarding jobs or tasks assigned to them or which they are following. Email notifications allow users to learn about important events without having to manually check job status.

For example, some events that trigger email notifications are:

  • A task assigned to me is ready to be completed
  • A job that includes tasks assigned to me is initiated
  • A job that I owned and completed was reactivated by another user

Receive Email Notifications

By default, all users will receive email notifications about events that occur regarding jobs and tasks that they are part of, or are following.

Users can choose to opt out of all email notifications by disabling this setting.

Select Settings from the user menu, then check the box for Receive email notifications to receive them. Uncheck the box to disable receiving email notifications.

Click Finish to save this setting.

Related Topics




Edit Jobs and Tasks


This topic covers editing and updating workflow jobs and tasks.

Edit Job Description

Edit the job description by clicking it directly in the job overview section. Enter the new description in the popup and click the button to update it.

Update Job Details

In the Job Overview panel you can edit many common job details including Start and Due Dates, Assignee of the job as a whole, Priority, and which users to notify. Click Update to save your changes.

The name of the job cannot be edited here, instead, select > Edit Job.

Edit the items on the Job Details and Priority panel. You can also edit items here that are also editable on the overview panel. Click Finish Updating Job when finished.

Edit Tasks: Add, Reorder, Edit, Delete

Note that you cannot edit any tasks that have been completed. You also cannot edit tasks in a job that was created from a template, or in a job from which a template was created. A banner message and icons will inform you when tasks are not editable. The process in this section applies to non-template jobs where all tasks are editable until they are completed.

To adjust the tasks involved in the job, select Edit Job from the three bar menu. You will see the same interface you used to define job tasks.

  • Click the Define Job Tasks section.
  • Any tasks that have been completed (or are part of a template) cannot be changed and will be shown with a icon.
  • Add more tasks via Add Task. (You cannot add tasks to a job created from a template.)
  • Reorder tasks by dragging and dropping the six-block handle on the left.
  • Delete a task by clicking the icon on the right.
  • Use the expansion icon to open the panel for changing descriptions or task due dates.

Make the necessary changes and click Finish Updating Job when you are finished.

Edit Samples Assigned to a Job

While editing a job, you can use the Assign Samples section to adjust the set of samples within the job. Follow the instructions in this topic to search for samples within the job wizard. If you only need to add or remove samples, it may be easier to follow the steps below to add or delete samples from jobs.

Add Samples to a Job

From the main menu, click the name of the type of samples you wish to add to open the grid of available samples. Select the desired sample(s) using the checkboxes and select Jobs > Add Samples to Existing Job. In the popup, select the desired job by name from the dropdown. Click Add to Job.

If you attempt to add samples that are already included in the job, they will be skipped automatically and only new samples will be added.

Delete Samples from a Job

Open the job and click the Samples tab. Select the sample(s) you wish to delete and select Manage > Remove Samples from Job.

Add or Delete Files from a Job

To see and change files attached to a job, you can use the Attach Files section within the job editor, or click the Files tab near the top of the page. Files attached will be listed, with details about who attached them and when.

Add a new file by clicking Attach File and using the Select file or drag and drop here box. Click Upload to attach the selected file(s).

Delete a file by clicking the red icon for the desired file.

Reactivate Closed Task

To reactivate a closed task, click the Tasks tab in the upper left, then click the name of the closed task to select it. It will be shown with a checked box icon, in the following image, "Prepare Samples" is in a closed state.

Select Reactivate Task from the drop down menu to reactivate it.

You will be asked to confirm the action, and when completed, the checked box icon will disappear and the task will be restored to an "In Progress" state. You may also want to leave a comment when you reactivate a task, explaining the action. Enter the comment in the box and click Comment to save it.

Reactivate Completed Job

If you need to reactivate a job that was marked completed, find it by opening the Workflows page from the main menu and clicking Completed Jobs. Click the desired job name to open it.

Select Reactivate Job from the drop down menu. You will be asked to confirm the action.

When you reactivate a job, the last task of the job is also automatically reactivated. If you would like to reactivate additional tasks, follow the steps above.

Delete Job

To delete a job that is no longer necessary, select it from the list, then select > Delete Job.

Related Topics




Manage Users and Permissions


This topic covers management of user accounts in LabKey Sample Manager. Only Administrators can perform these actions via the Administration option on the user menu. For a walkthrough of this process, follow the Sample Manager tutorial step: Tutorial: Add Users and Assign Roles.

Add Users

To add one or more new users, an administrator first selects Administration from the user menu, then clicks Create.

In the popup:

  • Enter one or more email addresses, each on it's own line for each user you want to create.
  • Select the desired Role for the users you are creating:
    • Reader (default): Can read but not edit anything in LabKey Sample Manager.
    • Editor: Can enter new information and edit some existing information.
    • Administrator: Can perform all administrative functions.
    • Note that all users added at once are assigned the single role you select. You can change these role assignments later.
  • Leave the box checked if you want to Send notification emails to all new users. These invitation emails will include a link for the new user to create a password and log in.
    • If you uncheck this box, no email will be sent.
  • Optional Message: If you have checked the box to send email, you can add an optional additional message to include in the invitation email to your new users.
  • Click Create Users.
You will see the new user(s) added to the grid.

The new user will receive an email with a link to set a password and log in. If the new user should lose their initial invitation email, an admin can trigger the sending of another by selecting the row for that user and clicking Reset Password in the user details. See below.

Manage Users

To manage users, an administrator selects Administration from the user menu.

You will see a grid of the active users already present on your server. You can use search, sort, and filter options on this user grid.

View User Details

To view the details for any user in the grid, check the box for that user. Details including effective roles are shown in a panel to the right.

From this panel, an administrator can click the buttons at the bottom to perform these actions on this individual user.

  • Reset Password: Send this user an email with a link to set a new password in order to access the site.
  • Deactivate
  • Delete
Click the user's Display Name in the grid to see even more details for that user.

Deactivate Users

Deactivated users may no longer log in, but their display name and group membership information will be retained for display and audit purposes. If the user is reactivated at a later time, this information will be restored. Deactivation is the recommended action for former employees, for example.

To deactivate a user, an administrator has two options:

  1. Check the box to select a single user you want to deactivate. Click Deactivate in the User Details panel on the right.
  2. You may also select one or more users simultaneously using the checkboxes in the grid, then select Manage > Deactivate Users.
For either option, you will be asked to confirm that this is the action you want to take by clicking Yes, Deactivate in a popup.

Delete Users

Deletion of a user is permanent and cannot be undone; it is generally not recommended. A deleted user's display name will no longer be shown with any assignments or actions taken by that user. A deleted user cannot be reactivated to restore any information.

Instead of deleting, deactivation is recommended for any user who has performed any work in the system in the past.

One scenario in which deletion might be appropriate is if you originally create a new user with an incorrect email address or other error.

To delete a user, an administrator has the same two options as for deactivation:

  1. Check the box to select a single user you want to delete. Click Delete in the User Details panel on the right.
  2. You may also select one or more users simultaneously using the checkboxes in the grid, then select Manage > Delete Users.
You will be warned that deletion is permanent and need to click Yes, Permanently Delete to proceed.

View Inactive Users

Notice that the grid reads Active Users by default. To view the grid of deactivated users instead, select Manage > View Inactive Users.

You can check a box to see details for inactivated users, and buttons are offered to Reactivate and Delete a single user.

On the grid of interactive users, the Manage menu actions are also slightly different. You can select one or more rows to reactivate or permanently delete users. You can also switch back to the grid of active users.

Use Manage > View All Users from either view to see the combination of active and inactive users.

Manage Roles and Assignments

Once users have been defined, an administrator can assign them one of the three available permission levels:

  • Editors: May add new information or edit data related to samples, assays, and jobs.
  • Readers: Have a read-only view of the application.
  • Administrators: Have full control over the application. This includes user management, permission assignments, and creating and editing sample types, assays, and job templates.

Assign Editor and Reader Roles

Reopen user management if you closed it by selecting Administration from the user menu. Click the Permissions section.

To add a user to either the Editor or Reader role:

  • First click the role section. You'll see the current members of that role.
  • Click the Add member dropdown and select each user to add by email address.
    • Selected users will be shown in the panel for the role as you go.
    • Each time you select a user, the details for that user will be shown on the right to assist you.
  • In the image below, the Editor role is being granted to users named "team lead" and "lab technician"; the Reader role is being granted to the "reviewer".

Click Save.

Assign Administrator

Administrators have full control over the application. This includes user management, permission assignments, and creating and editing sample types, assays, and job templates. The first user login created on the Sample Manager application is always an administrator. To assign the administrator role to others, any administrator can choose the Settings tab.

Click the Administrators panel and use the Add member dropdown to select the user to assign the administrator role.

Remove Users from Roles

To remove a level of access for a given user, reopen the interface for granting that role and click the X for the user you want to delete from the role. Removing a user from a role does not deactivate or remove the user account itself.

A note about role-based permissions: Users can be assigned multiple roles in the system and each is independent. If a user is both Editor and Reader, removing them from the Reader role will not in fact remove that user's ability to read information in the system, because they also have that access via the Editor role.

Related Topics




Create a Job Template


Using job templates makes the creation of many similar workflow jobs simpler and more consistent. A template can include a common set of procedures and tasks, and new individual jobs can be created from this common template and edited or refined as needed.

The job template creation wizard is very similar to the steps involved in creating a new individual job, with the exception that samples and job details will be added to an individual job separately. No work is assigned within a template. You can also create a template during the process of creating an individual job, as described in Start a New Job.

Create a Job Template

To create a new job template:

  • Select Workflow from the main header menu.
  • Click Create, then select Job Template.

Click each section in the wizard to define template details and job tasks, and attach any files that should always be included when a job is created from this template.

After completing all sections, click Finish Creating Template to save.

Job Template Details

Enter the Template Name and Description. The name should be unique enough to help users find it on a menu.

Define Job Tasks

Click the Define Job Tasks panel and enter the tasks. For each, enter Task, select any Assays to Perform as part of that task. One task at a time can be expanded to enter a description if needed.

Use Add Task to add additional tasks.

Attach Files

Click the Attach Files panel to upload any files that should be available to any jobs created from this template.

Finish Creating Template

Click Finish Creating Template when finished. You'll see the new template overview.

Notice in the upper left that there are tabs for viewing any Files associated with the template and for viewing any Jobs created using it.

Related Topics




Manage Jobs and Templates


This topic covers options available for administrators to manage jobs and templates. You will find the active lists of jobs and templates and manage options in the Workflow section.

Manage Jobs

From the home dashboard, click Jobs Home or from anywhere in the application, select Workflow List from the main menu.

Click All Jobs to see the full list of jobs. Other tabs provide subsets.

Edit Jobs

To open an individual job for editing, click the Job Name. Details of editing jobs and tasks are covered in this topic: Edit Jobs and Tasks

Delete Jobs

To delete one or more jobs, use the checkboxes on the Job List to select jobs for deletion, then click Manage > Delete Jobs.

You can also delete a single job by opening it and selecting Delete Job from the menu in the upper right.

Manage Templates

Templates are managed from the Job Templates tab on the Jobs List.

Open an individual template by clicking it's Name. The template overview shows a summary of tasks and assays. In the upper left, you can click the Files tab to see files that are part of the template and on the Jobs tab you'll see a listing of jobs created from this template.

Edit Template

To edit a template, open it as shown above and select Edit Job Template from the menu.

You can edit the Name and Description, but not the tasks associated with the template.

Editing a template does not change any jobs that have already been created from the previous version of the template.

Delete Template

To delete a template, open the details page as shown above and select Delete Job Template. Once a job has been created from a template, you can no longer delete it and this option will be inactive.

There is no option for deleting multiple templates at once.

Workflow Heatmap

You can also view workflow jobs in a heatmap format. There is a row for tracking the count of jobs created from each template and all jobs not created from templates are grouped together in an additional row, "Jobs not from templates."

Related Topics