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CTG

CTG is a Ruby client library for interacting with the ClinicalTrials.gov API. It allows you to fetch and query clinical study data, including study metadata, search areas, study sizes, field values, and more. The library supports both JSON and CSV response formats, with built-in support for pagination and advanced querying.

Installation

Add this line to your application's Gemfile:

gem 'ctg'

And then execute:

bundle install

Or install it yourself as:

gem install ctg

Usage

Initializing the Client

To start using the CTG, first create a new client instance:

require 'ctg'

client = CTG.new

Fetching Studies

You can fetch studies using the studies method. This will return a CTG::Response object that you can query.

response = client.studies('query.term' => 'cancer')
studies = response.query('studies')
puts studies

Fetching a Single Study by NCT Number

You can fetch a single study by its NCT number:

response = client.number('NCT04050163')
study = response.query('nctId')
puts study

Fetching Study Metadata

To fetch metadata information about study fields:

response = client.metadata
metadata = response.data
puts metadata

Handling Pagination

If your query returns multiple pages of results, you can fetch the next page using the next_page method:

response = client.studies('query.term' => 'cancer', 'pageSize' => 5)
puts response.query('studies')

next_page_response = response.next_page
puts next_page_response.query('studies') if next_page_response

Querying the Response

You can query JSON responses using keys or XPath expressions:

response = client.number('NCT04050163')
nct_id = response.query('nctId')
puts nct_id  # Outputs 'NCT04050163'

For CSV responses, query by column name:

response = client.number('NCT04050163', format: 'csv')
nct_ids = response.query('NCT Number')
puts nct_ids

Finding a Specific Key in JSON Data

You can find the first occurrence of a specific key within the JSON data using the find method:

response = client.number('NCT04050163')
nct_id = response.find('nctId')
puts nct_id  # Outputs 'NCT04050163'

CTG::Query Object

The CTG::Query class is designed to help you build complex queries for searching clinical studies on ClinicalTrials.gov. It provides a convenient way to add different query parameters and filters, allowing for advanced search capabilities.

Creating a Query

To start building a query, you first need to create an instance of the CTG::Query class:

query = CTG::Query.new

Adding Query Parameters

The CTG::Query object allows you to add various search parameters using method chaining. Below are the available methods:

condition(condition)

Adds a condition or disease to the query.

  • Parameter: condition (String) - The condition or disease to search for.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.condition('diabetes')

term(term)

Adds additional search terms to the query.

  • Parameter: term (String) - Additional search terms.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.term('lung cancer')

location(location)

Adds a location filter to the query.

  • Parameter: location (String) - The location term to filter results by.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.location('New York')

title(title)

Adds a title or acronym to the query.

  • Parameter: title (String) - The title or acronym to search for.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.title('COVID-19 Vaccine')

intervention(intervention)

Adds an intervention or treatment to the query.

  • Parameter: intervention (String) - The intervention or treatment to search for.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.intervention('remdesivir')

outcome(outcome)

Adds an outcome measure to the query.

  • Parameter: outcome (String) - The outcome measure to search for.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.outcome('survival rate')

collaborator(collaborator)

Adds a sponsor or collaborator to the query.

  • Parameter: collaborator (String) - The sponsor or collaborator to search for.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.collaborator('IQVIA')

sponsor(lead_sponsor)

Adds a lead sponsor to the query.

  • Parameter: sponsor (String) - The lead sponsor to search for.
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.sponsor('National Institutes of Health')

study_id(study_id)

Adds a study ID filter to the query.

  • Parameter: study_id (String) - The study ID or IDs to search for (comma- or space-separated).
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.study_id('NCT01234567')

status(*statuses)

Adds an overall status filter to the query.

  • Parameter: statuses (Array) - The list of statuses to filter by (e.g., ['RECRUITING', 'COMPLETED']).
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.status('RECRUITING', 'COMPLETED')

page_size(size)

Specifies the number of results per page.

  • Parameter: size (Integer) - The number of results to return per page (max 1000).
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.page_size(50)

format(format)

Specifies the format of the response.

  • Parameter: format (String) - The format of the response ('json' or 'csv').
  • Returns: The updated CTG::Query object.
query = CTG::Query.new.format('json')

Retrieving Query Parameters

Once you’ve built your query, you can retrieve the complete set of query parameters as a hash:

query_params = query.params

This params method returns a hash of all the query parameters that have been set.

Example: Building a Complex Query

Here’s an example of how you might build a more complex query using method chaining:

query = CTG::Query.new
  .condition('diabetes')
  .term('insulin')
  .location('California')
  .status('RECRUITING')
  .page_size(10)
  .format('json')

# Use the query in a client request
response = client.studies(query)
puts response.query('studies', 'protocolSection', 'outcomesModule', 'secondaryOutcomes' )

In this example, the query is set to search for recruiting studies related to diabetes and insulin in California, returning results in JSON format with a page size of 10.

Finding All Occurrences of a Key in JSON Data

If you need to find all occurrences of a specific key within the JSON data, use the find_all method:

references = response.find_all('references')
puts references

Running Tests

To run the tests, use RSpec:

rspec

This will run all the tests located in the spec/ directory and report on their success.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/trialize/ctg.

License

This library is available as open source under the terms of the MIT License. Copyright 2024 Leonid Stoianov. Copyright 2024 Trialize.