Advanced Tutorial: Python API: /Documentation/Archive/12.2

Advanced Tutorial: Python API

Overview

[Live Demo] [Python API Module + Documentation]

Caution

This page contains preliminary content to guide you through setting up the Python API Tutorial on a server where you have project admin permissions.

Please note that this is an advanced tutorial. If you'd like a lighter intro to the Python API, just use the samples included in the labkeypython.py module file itself. You can use executeSql() and selectRows() on the PythonProject on LabKey Online without any further setup. The tutorial below involves more setup to allow alteration of data on a LabKey Server, not just retrieval of data, plus demo a real-world scenario.

Scenario

Your test labs have collected salmonella samples in the field. These labs sequence 7 indicator genes for each of the collected samples.

You want to use these 7 indicator genes to identify the strain type of each sample. The strain type is an identifier that lets you compare these samples with very similar samples.

Once you know a sample's strain type, you can use existing datasets to look at where this strain type has been collected before, in which species, etc.

Data used in this scenario come from the public MLST Databases at the ERI, University College Cork

How LabKey Server can be used in this scenario

LabKey Server helps you centralize data management through a web-based portal that can be used by end-labs, study managers, statisticians, PIs, etc. End labs can upload their data files, then central study managers or statisticians can import the data in these files into the LabKey database in a structured way. In this tutorial, sample information is analyzed using a python script that leverages existing sample/reference data that has already been uploaded to the system.

Data analysis steps in our python script

The python analysis script used in this tutorial does the following:

Get the names of all your samples (runs)
For each sample

Get its 7 gene sequences
For each of 7 genes

Figure out which reference gene version # matches
Keep a list of these versions #

Match list of 7 gene version #s to matching strain type #
Update sample results table:
Sample name, strain type #, # related strains, reference strain

Tutorial

Set up portal

Install LabKey Server or log on to your personal test project on LabKey Online. If you need a project, email eknelson@labkey.com
Add a folder on your server (or to your project on LabKey Online)
Select "Assay" as the folder type
On the new portal page, add the following web parts:

Get files

Download labkeyquery.py and labkeycredentials.txt from the Python API documentation page.
Download tutorial files: LabKeyDemoFiles.zip

Extract .zip
Grab the files in the LabKeyDemoFiles///API///SalmonellaTutorial directory.

Move all the labkeyquery.py, labkeycredentials.txt and straintypeX.py files into the same directory as your python installation.
Start python and make sure you can see these files. Type:

import os
os.listdir(os.curdir)

Doesn't matter where you keep the .xls and other files from the SalmonellaTutorial folder, but note the directory.

Edit the default tutorial files

Update the straintypeX.py file with:

Your server's URL
The path of the assay folder you just set up. These appear only once at the beginning of the file.

Update the labkeycredentials.txt file with:

The machinename of your LabKey Server installation.
The username/password you're using on this server as a project admin.

Note that if you're running LabKey Server locally, the URL and machinename of your server may look something like this:

http://localhost:8080/labkey

Set up lists

Import the list archive.

Upload files to server

Upload sample files to the files web part

Import 1 file to create an assay design

In the files web part, select one file and click Import File
Enter "Salmonella Sequence Assay" as the assay design name
Yes to everything else

Import all your other data files to this assay design

Select all of the files you haven't used yet in the files web part.
Click Import Files
Select the radio button for the "Salmonella Sequence Assay" design
At the bottom of each of the following pages, Click "Save and Import Next File"
On the last page, click "Save and Finish"

Run the script

Go back to where you have Python running and type:

import straintypeX.py  (Note: Replace X with the current version number of this file)
straintypeX.analyze()

You should see results scroll onto the screen.

Explore results

Go to the portal page of the folder you've set up.
In the list web part, click the "Sample Results" list.
All the data you see in this list was put there by the script you just ran.
Create custom views (draw in related tables), R views (e.g., a histogram), etc using your results.

Notes for Assay version of this tutorial

This section is still under construction. Information here is just in draft form - notes, really.

Do all of the steps listed in the previous section through "Upload files to server." Now, instead of following the next steps, use these:

Alternative 1: Set up assay design using shortcut

Import xar to define assay

Alternative 2: Set up assay design and import first set if data:

In the files web part, select a data file and choose to create a new GPAT-type assay design Enter a name for the assay design Open the assay designer In the Assay Properties section, check the box next to “Editable Runs” and “Editable Results”

Delete all batch properties

ParticipantVisitResolver
TargetStudy

Add run properties:

Name: StrainType

Type: lists.Strain Type Genes

Name: RelatedStrainTypes

Type: Integer
URL: https://hosted.labkey.com/list/PythonProject/SalmonellaV1/grid.view?listId=352&query.STRAINTYPE~eq=${STRAINTYPE}

Name: Reference Strain

Type: lists.Strain Metadata (String)

For data fields leave most of the fields, but delete a few defaults:

ParticipantID
VisitID
Data

Save assay design and finish uploading your assay run data

LabKey Support

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