- Course overview
- Search within this course
- Overview of key IMPC concepts and tools
- Introduction to the Solr API: accessing IMPC data programmatically
- What is Apache Solr?
- Important definitions: query, field, core, document, parameter
- Quiz 2: get yourself familiar with Solr terminology
- What is the difference between an IMPC parameter and a Solr parameter?
- Using simple Solr syntax in your browser
- Output of the simplest request in your browser
- A Python module to access IMPC data: installation and available functions
- Quiz 3: explain Solr request
- Solr query syntax: simplified explanation
- How to use the solr_request function from the impc-api python package
- How to perform a query: q parameter
- Exercise 1: getting familiar with the core
- How to request a limited number of documents: rows parameter
- Exercise 2: requesting three documents
- How to get specific fields: fl parameter
- Exercise 3: selecting specific fields
- Quiz 4: basic Solr parameters
- Filtering data in Solr: narrowing down your results
- How to query a specific field: filter by value
- Exercise 4: filtering by a single field
- How to filter numbers: range search
- Exercise 5: changing the p-value threshold
- How to combine multiple filters: Boolean operators
- Exercise 6: applying multiple filters
- How to exclude data: NOT operator
- Why parentheses are important: combine multiple Boolean operators
- Quiz 5: Boolean operators
- How to handle with null values: exclude empty fields
- Exercise 7: explore null values
- Advanced Solr query techniques: faceting and iterating over entities
- Understanding IMPC data: resources and assistance
- Your feedback
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Exercise 8: download the data
We have an example of a query using the solr_request function below. Download this data using the batch_solr_request function in JSON format.
Go to exercise 8 in the Google Colab. Once you’ve finished Exercise 8 in the Google Colab, return here to continue the tutorial.
Show the correct answer
df = batch_solr_request(
core='genotype-phenotype',
params={
'q': 'marker_symbol:Xrcc5',
'fl': 'marker_symbol,marker_accession_id,parameter_name,parameter_stable_id,p_value,zygosity'
},
download=True,
batch_size = 200,
filename='xrcc5_output'
)