Repurposing a Process to Upload Indexes

Compatibility: API version 2

Uploading indexes (reagent types) into BaseSpace Clarity LIMScan be done 3 different ways:

1. Manually adding the indexes one at a time using the Operations interface.

2. Uploading an XML data file using the config slicer.

3. Using the API directly.

There is no "out of the box" method to quickly and easily upload a CSV file of many indexes to the LIMS. Adding the indexes one at a time is not quick, and using the config slicer requires admin privileges, knowledge of the correct XML file format, and the command line.

Solution

This example enables Clarity LIMS lab users to upload a CSV file containing new indexes and, through an EPP trigger, instantly create the indexes in Clarity LIMS. This example provides the provides the functionality included with the config slice, including preventing the indexes from being created if there is already an index with the same name in the system as well as ensuring the sequence only contains a valid nucleotide sequence (composed of A,G,T and C).

Protocol Step Configuration

In this example, a protocol step is repurposed as a mechanism to upload indexes. The protocol is configured to not produce any analyte outputs, and a single shared output file is used as the placeholder to upload the CSV file containing the indexes. The step is configured to permit use of a control sample, which allows the user to begin the step without any sample inputs.

Parameters

The script accepts the following parameters:

-f	The LUID of the file placeholder for the CSV file (Required)
-u	The username of the current user (Required)
-p	The password of the current user (Required)
-s	The URI of the step that launches the script - the {stepURI:v2} token (Required)
-l	The LUID of the file placeholder for the Log file (Required)

An example of the full syntax to invoke the script is as follows:

/usr/bin/python /opt/gls/clarity/customextensions/addindexescsv.py -u {username} -p {password} -s {stepURI:v2} -f {compoundOutputFileLuid0} -l {compoundOutputFileLuid1}

User Interaction

The lab scientist begins the step with only a control in the ice bucket. The user uploads the CSV file to the placeholder on the record details screen, and pushes the button to trigger the script.

About the Code

The main method in the script is importIndexes(). This method first calls the function downloadfile() which finds the location of the CSV file on the Clarity LIMS server and reads the content into memory.

The script then generates an XML payload for each index, checks the nucleotide sequence against the acceptable characters, and POSTs to the /api/v2/reagenttypes endpoint. If an index with the same name is already present in the LIMS, the log will be appended with the exception.

This example script produces a log which tracks which indexes were not added to the system as well as the reason. The log displays how many indexes were successfully added to the system and the total number of indexes included in the CSV file.

Assumptions and Notes

• You are running a version of Python that is supported by Clarity LIMS, as documented in the Clarity LIMS Technical Requirements.

• The attached files are placed on the LIMS server, in the /opt/gls/clarity/customextensions folder.

• You will need to update the HOSTNAME global variable such that it points to your Clarity LIMS server.

• The example code is provided for illustrative purposes only. It does not contain sufficient exception handling for use 'as is' in a production environment.

Attachments

example_Indexes.csv:

6KB

ClusterBCL.py

addindexescsv.py:

3KB

addindexescsv.py