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NanoLIMS v2.0 Manual For Admin

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cheinle edited this page Jan 17, 2017 · 5 revisions

#Table of Contents

Creating Admin User

In your web browser go to http://[myipaddress]/[path from document root to nanolims folder]/NanoLIMS/login.php Ex: http://localhost/NanoLIMS/login.php

  1. Create New User
  2. Login With Default NanoLIMS Admin User
  3. Activate New Admin User
  4. Deactivate NanoLIMS Default Admin User

###Create New User

Select ‘Create an account’

Enter account details and check the checkbox ‘Sign-Up As System Admin’

###Login With Default NanoLIMS Admin User

NanoLIMS comes with an admin user pre-loaded.

Username: [email protected]
Password: admin

###Activate New Admin User
Go to 'Admin Tools'
Select 'User Info'
Select 'Update User Login'

Change Login Allow (Y/N) to 'Yes' for new user
If User role is not set to 'Admin', switch at this time to make yourself an Admin

###Deactivate Default NanoLIMS Admin User
Go to 'Admin Tools'
Select 'User Info'
Select 'Update User Login'

Change Login Allow (Y/N) to 'No' for [email protected]

Creating More Users

Admins can create new users in the webUI:
Go to 'Admin Tools'
Select 'User Info'
Select 'Add Users'

Alternatively, users can register using 'Create an account' feature on login page. An email will be sent to admin to activate their account

How To Customize Colors and Homepage Picture

Colors can be edited in config/css.php

Homepage photo can be edited in body.homepage{} block of Home Page section. Place photo in images directory

Background color can be edited in body{} block of Home Page section

Navigation bar colors can be edited in Navigation Bar section

Login page background can be changed in aquired/assets/img/bg. Login rotates through 4 images. Upload image and rename to 1.jpg,2.jpg,3.jpg, or 4.jpg

Set-up Freezer Storage

Select ‘Admin Tools’ from main toolbar Select ‘Add Manipulate Dropdown Options’ from dropdown Select ‘Add Freezer/Drawer’ from dropdown

To add Freezer Names

Select ‘Add Freezers’ from dropdown

Enter Freezer name in ‘New Freezer Name’ input

Click ‘Submit Button

To add Drawer Names

Select ‘Add Drawers’ from dropdown

Enter Drawer name in ‘New Drawer Name’ input

Click ‘Submit Button

To link Drawers to Freezers

Select ‘Connect Drawers To Freezers’ from dropdown

Select a Freezer Name from ‘Pick A Freezer’ dropdown for which you would like to link specific drawers to

Select a Drawer Name from ‘Pick A Freezer’ dropdown for which you would like to assiciate with the above named freezer

Click Submit button. Repeat as needed

Set-up Sample Types

Select ‘Admin Tools’ on the main toolbar
Select 'Manipulate Dropdown Options'
Select ‘Add Sample Type’

Fill in form. Note that Sample Type ID will be used to build the unique sample names ([YYYY/MM/DD][Project Name][Sample Type][3-digit sample number]). This allows the user to quickly identify which sample type it is.

For example:
Sample Type Name: Fungal
Sample Type ID: F

Sample Name: 2015/10/21MyFirstProjectF001

Note: Sample types P (pooling) and B (sterilization blank) come already populated. Blank-Sterilization sample types are currently are set to have no sampling duration regardless of what is input

Approve Project Names As Needed

Once a user has requested a project name to be added to the database, the admin will be sent an email with this information

Login and select ‘Admin Tools’
Select ‘Add Manipulate Dropdown Options’ from dropdown
Select ‘Add Project Name’

Fill out information using the information in the email sent to you. Email user separately, before entering any information, if there are any questions. An email will automatically be generated to notify the user that their project name has been approved and entered, once you submit the form

Add Dropdown Options

Admins can quickly add options to any dropdown option used for sample entry

Select ‘Admin Tools’
Select ‘Add Manipulate Dropdown Options’ from dropdown
Select ‘Add Dropdown Options’ from the dropdown

Choose desired table to add to from the Table Name dropdown (ex: Media Type)

Enter in the name of the media

Press the Add button

Note : Users can also add a to limited amount of fields on their own under ‘Update Sample Fields’

Update Dropdown Options

Admins can update options to any dropdown option used for sample entry. This option would most likely be used to correct typing errors. Updates will update all old entries in the database automatically

Select ‘Admin Tools’
Select ‘Add Manipulate Dropdown Options’ from dropdown
Select ‘Add Dropdown Options’ from the dropdown

Choose desired table to update from the Table Name dropdown (ex: Media Type)

Select the entry that you would like to update from the ‘Entry To Update’ dropdown

Correct the entry in the ‘Edit Entry Here’ Box

Press the Update button

Delete Dropdown Options

Admins can delete options to any dropdown option used for sample entry by changing their visibility in the database. This option may be used if an option is no longer being used and should not be chosen. Updates to visibility will remove the option from being chosen but does not change any sample entries which have been entered with the option that is being removed. Note: Any option that is ‘deleted’ can be made visible again if needed by selecting ‘Option 2: Make Visible’

Select ‘Admin Tools’
Select ‘Add Manipulate Dropdown Options’ from dropdown
Select ‘Delete Dropdown Options’ from the dropdown

Choose desired table to update from the Table Name dropdown (ex: Media Type)

Select the entry that you would like to delete

Press the Delete button

Create Custom Fields

Admins can add custom fields to record custom information about their samples on a per sample basis. These custom fields will appear in the 'User Created Fields' in both Insert Sample and Update Sample.

NanoLIMS currently allows admins to add custom numeric and text entries (free text or dropdown).

To create a custom field:

Enter a Label Name (include units if needed)

Select Field Type (Numeric Input, Text Input, or Text Dropdown)

If Text Dropdown, enter dropdown options seperated by semi-colon in ‘Enter Dropdown Options’

Select if the new field is to be required input for each sample.

**Created Fields can be edited and visibility changed (non-permanent delete) using the ‘Update Dropdown Options’ and ‘Change Visibility’ functions as noted above

Notes for Admin

  • Blank-Sterilization sample types are currently are set to have no sampling duration regardless of what is input

  • No Sample Deletion - Samples cannot be deleted via the web-ui at this time. However, samples entries that were entered incorrectly or by mistake can be edited using the 'update samples' option to change many fields including date/time, project name, project type, and sample number (as long as it does not exist already for the given project)

  • Read submission recording - Read submission function is only for keeping a record of reads submitted public database, it does not actually create the formal submission of the reads to that database

  • No Sequencing submission update - Currently there is no form to update past sequencing submission info

  • There is no admin log file

  • Admin is responsible for appropriate database back-up (If using suggested AWS LightSail, follow snap-shot instructions)

Please see NanoLIMS v2.0 Manual For Developers for more information

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