Pathling

https://pathling.csiro.au/docs
Admin
Pathling is a set of Apache Spark-based tools that simplify health data analytics by enabling...
Tokens:658,606
Snippets:3,807
Trust Score:5.8
Update:9 months ago
Show doc for...
Tokens:
Raw
### Start Pathling Server using Docker Compose

Source: https://pathling.csiro.au/docs/7.2.0/server/getting-started

This command initiates the Pathling server based on the configurations defined in the 'docker-compose.yml' file. This includes setting up persistent volumes and environment variables.

```shell
docker-compose up
```

--------------------------------

### Install Spark/Hadoop using pathling_install_spark() (R)

Source: https://pathling.csiro.au/docs/r/reference/pathling_install_spark

Installs the version of Spark/Hadoop defined in the package metadata using the `sparklyr::spark_install` function. This function returns a list containing information about the installed Spark version.

```r
pathling_install_spark()
```

--------------------------------

### Run Pathling with Docker

Source: https://pathling.csiro.au/docs/7.2.0/server/getting-started

This command starts a basic, non-persistent instance of Pathling using the latest Docker image. It maps port 8080 and automatically removes the container upon stopping. Data is not persisted.

```shell
docker run --rm -p 8080:8080 aehrc/pathling
```

--------------------------------

### Install BasicTeX and Freetype on MacOS

Source: https://pathling.csiro.au/docs/r/index

Installs BasicTeX and Freetype using Homebrew, which are prerequisites for generating PDF manuals on MacOS.

```shell
brew install basictex
brew install freetype
```

--------------------------------

### Install Pathling Import CLI Tool

Source: https://pathling.csiro.au/docs/7.2.0/libraries/javascript/pathling-import

This command installs the Pathling import tool globally using NPM. This tool allows you to run the import process from the command line, configured via environment variables or a JSON file.

```bash
npm -g install pathling-import
```

--------------------------------

### Example: Pathling Context Initialization (R)

Source: https://pathling.csiro.au/docs/r/reference/pathling_connect

Demonstrates how to create a Pathling context using the pathling_connect function. It shows examples of connecting with an existing Spark connection and creating a new one if none is available.

```r
if (FALSE) { # \dontrun{
# Create PathlingContext for an existing Spark connecton.
pc <- pathling_connect(spark = sc)

# Create PathlingContext with a new Spark connection.
pc <- pathling_connect()
spark <- pathling_spark(pc)
} # }
```

--------------------------------

### Construct Path to Pathling Example Data (R)

Source: https://pathling.csiro.au/docs/r/reference/pathling_examples

The `pathling_examples` function constructs a platform-independent path to the package's example data. It takes character vector arguments representing path components. The function returns a string representing the full path to the specified example data file.

```R
pathling_examples(...)
pathling_examples('ndjson', 'Condition.ndjson')
```

--------------------------------

### Create Pathling Notebook Docker Image (Dockerfile)

Source: https://pathling.csiro.au/docs/7.2.0/libraries/installation/spark

This Dockerfile example demonstrates how to create a custom Docker image for a Pathling notebook. It starts from a base Jupyter all-Spark-notebook image, configures Pathling as a Spark package by appending to `spark-defaults.conf`, and then installs the Pathling Python package using pip.

```dockerfile
FROM jupyter/all-spark-notebook

USER root
RUN echo "spark.jars.packages au.csiro.pathling:library-runtime:[some version]" >> /usr/local/spark/conf/spark-defaults.conf

USER ${NB_UID}

RUN pip install --quiet --no-cache-dir pathling && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

--------------------------------

### Update and Install TeX Live Packages for R Manuals

Source: https://pathling.csiro.au/docs/r/index

Updates TeX Live and installs necessary packages like 'titling', 'framed', and 'inconsolata' fonts for building R package vignettes.

```shell
# Install texlive packages needed to build R package vignettes
sudo tlmgr update --self
sudo tlmgr update --all
sudo tlmgr install titling framed inconsolata
sudo tlmgr install collection-fontsrecommended
```

--------------------------------

### Install Pathling with Python

Source: https://pathling.csiro.au/docs/7.2.0/libraries/installation

Installs the Pathling Python package using pip. Requires Python 3.8+ with pip.

```bash
pip install pathling
```

--------------------------------

### systemBuilder()

Source: https://pathling.csiro.au/docs/java/index-all

Creates a builder instance for initiating a system-level bulk data export.

```APIDOC
## Static Method: systemBuilder()

### Description
Create a builder for a system-level export.

### Method
GET

### Endpoint
/api/bulk/export/system

### Returns
`BulkExportClient.SystemBuilder` - A builder object to configure and initiate a system-level export.
```

--------------------------------

### Install Pathling with R

Source: https://pathling.csiro.au/docs/7.2.0/libraries/installation

Installs the Pathling R package and its required Spark version. Requires R version 3.5.0 or higher.

```r
install.packages('pathling')
pathling::pathling_install_spark()
```

--------------------------------

### View Builder Build Methods

Source: https://pathling.csiro.au/docs/java/index-all

Documentation for the 'build' methods used in creating View instances.

```APIDOC
## build()

### Description
Builds and returns a new `FhirView` instance with the configured settings.

### Method
Method

### Endpoint
N/A

### Parameters
None

### Request Example
None

### Response
- **FhirView** - A new `FhirView` instance.

### Response Example
None
```

```APIDOC
## build()

### Description
Builds and returns a new `SelectClause` instance with the configured settings.

### Method
Method

### Endpoint
N/A

### Parameters
None

### Request Example
None

### Response
- **SelectClause** - A new `SelectClause` instance.

### Response Example
None
```

--------------------------------

### PathlingContext Initialization Options

Source: https://pathling.csiro.au/docs/python/pathling

This section outlines the configuration parameters that can be used to customize the behavior of a PathlingContext instance.

```APIDOC
## PathlingContext Configuration Options

This document details the various configuration parameters that can be passed to initialize a `PathlingContext`.

### Terminology Service Configuration

*   **terminology_verbose_request_logging** (boolean) - Enables verbose logging of requests to the terminology service. This logging is sent to the DEBUG level and is subject to the Spark logging level.
*   **terminology_socket_timeout** (integer) - Sets the maximum time in milliseconds the server should wait for incoming data from the HTTP service.
*   **terminology_retry_enabled** (boolean) - Controls whether to retry terminology requests that fail due to transient network or DNS issues.
*   **terminology_retry_count** (integer) - Specifies the number of times to retry failed terminology requests.
*   **accept_language** (string) - Sets the default `Accept-Language` HTTP header value. This allows specifying preferred languages for the terminology server to respond with, following RFC 9110 guidelines.

### Client Connection Configuration

*   **max_connections_total** (integer) - The maximum total number of connections the client can establish.
*   **max_connections_per_route** (integer) - The maximum number of connections allowed per specific route for the client.

### Caching Configuration

*   **enable_cache** (boolean) - Set to `false` to disable caching of terminology requests. Disabling the cache is generally not recommended.
*   **cache_max_entries** (integer) - Defines the maximum number of entries to store in the in-memory cache.
*   **cache_storage_type** (StorageType) - Specifies the type of storage to use for the terminology cache. Refer to `StorageType` for available options.
*   **cache_storage_path** (string) - The file system path for disk-based cache storage. This is required when `cache_storage_type` is set to 'disk'.
*   **cache_default_expiry** (integer) - The default expiry time in seconds for cache entries when the server does not provide an expiry value.
*   **cache_override_expiry** (integer) - An optional value to override the expiry time provided by the terminology server.

### Authentication Configuration

*   **enable_auth** (boolean) - Enables authentication for requests made to the terminology server.
*   **token_endpoint** (string) - The OAuth2 token endpoint URL for the client credentials grant flow.
*   **client_id** (string) - The client ID to use with the client credentials grant.
*   **client_secret** (string) - The client secret to use with the client credentials grant.
*   **scope** (string) - The scope value to use with the client credentials grant.
*   **token_expiry_tolerance** (integer) - The minimum number of seconds a token must have before expiry to be considered valid for use in terminology requests.

### Query and Data Processing Configuration

*   **explain_queries** (boolean) - Enables additional logging related to the query execution plan.
*   **max_unbound_traversal_depth** (integer) - Maximum depth for self-referencing structure traversals in repeat operations, controlling how deeply nested hierarchical data can be flattened.
*   **enable_delta** (boolean) - Enables the use of Delta for FHIR data storage. This is only supported when no `SparkSession` is provided.

### Remote Debugging Configuration

*   **enable_remote_debugging** (boolean) - Enables remote debugging for the JVM process.
*   **debug_port** (integer) - The port number for the debugger to listen on. Defaults to 5005.
*   **debug_suspend** (boolean) - If `true`, the JVM will suspend execution until a debugger is attached.
```

--------------------------------

### Get Subject Resource Type

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/execution/BaseResourceResolver

Abstract method to retrieve the primary resource type being queried. This is essential for understanding the context of a FHIRPath query, for example, 'Patient' in 'Patient.name.given'.

```java
@Nonnull public abstract Enumerations.ResourceType getSubjectResource()
Returns the subject resource type for this resolver.
The subject resource is the primary resource type being queried, such as Patient in a query starting with Patient.name.given.

Returns:
    The subject resource type
```

--------------------------------

### Configure Java Environment Variable on Databricks

Source: https://pathling.csiro.au/docs/libraries/installation/databricks

This snippet shows how to set the JNAME environment variable to enable Java 21 support on a Databricks cluster, which is a requirement for Pathling.

```plaintext
JNAME=zulu21-ca-amd64
```

--------------------------------

### Add Pathling Library to Scala SBT Project

Source: https://pathling.csiro.au/docs/7.2.0/libraries/installation

Adds the Pathling library runtime dependency to an SBT build configuration for Scala projects. Replace '[version]' with the desired Pathling version.

```scala
libraryDependencies += "au.csiro.pathling" % "library-runtime" % "[version]"
```

--------------------------------

### Configuration and Caching

Source: https://pathling.csiro.au/docs/java/overview-tree

Documentation for HTTP client configuration and caching mechanisms used within Pathling.

```APIDOC
## Configuration and Caching

### Description
Covers configuration options for the HTTP client and mechanisms for caching HTTP responses to improve performance.

### Components

- **HttpClientConfiguration**: Defines general HTTP client settings.
- **HttpClientCachingConfiguration**: Configures caching behavior for HTTP requests.
  - **HttpCacheConfigurationValidator**: Validates the HTTP cache configuration.

### Usage Examples

```java
// Configuring HTTP client caching
// HttpClientCachingConfiguration cachingConfig = new HttpClientCachingConfiguration();
// cachingConfig.setCacheDurationSeconds(3600);
// ... (code to apply configuration) ...
```
```

--------------------------------

### Add Pathling Library to Java Maven Project

Source: https://pathling.csiro.au/docs/7.2.0/libraries/installation

Adds the Pathling library runtime dependency to a Java Maven project's pom.xml file. Replace '[version]' with the desired Pathling version.

```xml
<dependency>
    <groupId>au.csiro.pathling</groupId>
    <artifactId>library-runtime</artifactId>
    <version>[version]</version>
</dependency>
```

--------------------------------

### build (with definition)

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/collection/CodingCollection

Returns a new instance of CodingCollection with the specified column and definition.

```APIDOC
## POST /api/coding/build/withDefinition

### Description
Returns a new instance of CodingCollection with the specified column and definition.

### Method
`public static CodingCollection build`

### Parameters
#### Request Body
- **columnRepresentation** (ColumnRepresentation) - Required - The column to use.
- **definition** (Optional<? extends NodeDefinition>) - Required - The definition to use.

### Request Example
```json
{
  "columnRepresentation": "exampleColumn",
  "definition": "exampleDefinition"
}
```

### Response
#### Success Response (200)
- **CodingCollection** (CodingCollection) - A new instance of `CodingCollection`.

#### Response Example
```json
{
  "message": "CodingCollection built successfully"
}
```
```

--------------------------------

### Run Pathling with Docker Compose and Persistent Storage

Source: https://pathling.csiro.au/docs/7.2.0/server/getting-started

This Docker Compose configuration sets up a Pathling instance with persistent storage for warehouse data and staging data. It also configures environment variables for the terminology server URL and CORS origins.

```yaml
version: "3"
services:
  pathling:
    image: aehrc/pathling:7
    ports:
      - 8080:8080
    environment:
      pathling.terminology.serverUrl: https://tx.somecompany.com/fhir
      pathling.cors.allowedOrigins: http://localhost:3000
    volumes:
      - pathling:/usr/share/warehouse
      - /home/me/data:/usr/share/staging
volumes:
  pathling:
    driver: local
```

--------------------------------

### AnsiSqlDataTypeBaseVisitor Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/views/ansi/generated/AnsiSqlDataTypeBaseVisitor

Initializes a new instance of the AnsiSqlDataTypeBaseVisitor class. This is the default constructor and does not require any parameters.

```Java
public AnsiSqlDataTypeBaseVisitor()

```

--------------------------------

### Java @ValidName Annotation Definition and Usage

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/views/validation/ValidName

Defines the @ValidName annotation for validating string fields. It specifies a regular expression pattern to ensure names start with a letter and contain only letters, numbers, and underscores. The example shows how to apply this annotation to a private field within a Java class.

```java
@Pattern(regexp="^[A-Za-z]\") @Constraint(validatedBy={}) @Target(FIELD) @Retention(RUNTIME) @ReportAsSingleViolation @Documented public @interface ValidName {
    String message() default "must be a valid name ([A-Za-z]\w*)";
    Class<?>[] groups() default {};
    Class<? extends jakarta.validation.Payload>[] payload() default {};
}
```

```java
public class MyClass {
    @ValidName
    private String name;
}
```

--------------------------------

### PathlingContext Creation Methods

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/library/PathlingContext

Provides static methods for creating PathlingContext instances with different configurations, including default setups, custom Spark sessions, and specialized configurations for encoding or terminology.

```APIDOC
## PathlingContext Creation

### Description
Methods for creating and initializing a `PathlingContext`, which serves as the entry point for Pathling operations.

### Static Factory Methods

#### `create()`

*   **Description**: Creates a new `PathlingContext` with a default setup for Spark, FHIR encoders, and terminology services.
*   **Method**: `static PathlingContext create()`
*   **Returns**: A new `PathlingContext` instance.

#### `create(SparkSession sparkSession)`

*   **Description**: Creates a new `PathlingContext` using a pre-configured `SparkSession`.
*   **Parameters**:
    *   `sparkSession` (SparkSession) - The Spark session to use.
*   **Method**: `static PathlingContext create(SparkSession sparkSession)`
*   **Returns**: A new `PathlingContext` instance.

#### `createInternal(SparkSession spark, FhirEncoders fhirEncoders, TerminologyServiceFactory terminologyServiceFactory)`

*   **Description**: Creates a `PathlingContext` with advanced configuration for testing purposes. This method is internal and intended for use within the library.
*   **Parameters**:
    *   `spark` (SparkSession) - The Spark session to use.
    *   `fhirEncoders` (FhirEncoders) - The FHIR encoders to use.
    *   `terminologyServiceFactory` (TerminologyServiceFactory) - The terminology service factory to use.
*   **Method**: `static PathlingContext createInternal(SparkSession spark, FhirEncoders fhirEncoders, TerminologyServiceFactory terminologyServiceFactory)`
*   **Returns**: A new `PathlingContext` instance with default query configuration.

#### `createForEncoding(SparkSession sparkSession, EncodingConfiguration encodingConfig)`

*   **Description**: Creates a `PathlingContext` using a supplied encoding configuration and a pre-configured `SparkSession`. This is a convenience method for cases where only the encoding functionality of Pathling is needed.
*   **Parameters**:
    *   `sparkSession` (SparkSession) - The Spark session to use.
    *   `encodingConfig` (EncodingConfiguration) - The encoding configuration to use.
*   **Method**: `static PathlingContext createForEncoding(SparkSession sparkSession, EncodingConfiguration encodingConfig)`
*   **Returns**: A new `PathlingContext` instance.

#### `createForTerminology(SparkSession sparkSession, TerminologyConfiguration terminologyConfig)`

*   **Description**: Creates a `PathlingContext` using a supplied terminology configuration and a pre-configured `SparkSession`. This is a convenience method for cases where only the terminology functionality (terminology UDFs) of Pathling is needed.
*   **Parameters**:
    *   `sparkSession` (SparkSession) - The Spark session to use.
    *   `terminologyConfig` (TerminologyConfiguration) - The terminology configuration to use.
*   **Method**: `static PathlingContext createForTerminology(SparkSession sparkSession, TerminologyConfiguration terminologyConfig)`
*   **Returns**: A new `PathlingContext` instance.

```

--------------------------------

### Get Upper Boundary Instant from FhirPathTime

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/FhirPathTime

Calculates and returns the upper boundary of the time value based on the precision of the FhirPathTime object. The upper boundary accounts for the finest granularity specified (e.g., milliseconds for fractional seconds). Examples illustrate how different precisions affect the upper boundary.

```java
@Nonnull public Instant getUpperBoundary()
Gets the upper boundary for this time value based on its precision. 
For example: 
      * `12` (HOUR precision) -> 12:59:59.999999999
      * `12:30` (MINUTE precision) -> 12:30:59.999999999
      * `12:30:45` (SECOND precision) -> 12:30:45.000000000
      * `12:30:45.123` (FRACS precision) -> 12:30:45.123 

Returns:
    the upper boundary as an Instant
```

--------------------------------

### Column Creation Methods

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/views/class-use/Column

Provides methods for creating Column instances, including static factory methods for collections and single columns, and methods for creating FhirView columns.

```APIDOC
## Static Factory Methods for Column

### Description
Static factory methods to create new `Column` instances.

### Methods

#### `static Column` collection(String name, String path)
Creates a new collection `Column` instance with required fields.

#### `static Column` single(String name, String path)
Creates a new non-collection `Column` instance with required fields.

### Request Example
```json
{
  "example": "Column.collection('myCollection', 'path.to.collection')"
}
```

### Response
#### Success Response (200)
- **Column** (object) - A representation of the created Column.

#### Response Example
```json
{
  "example": "Column representation"
}
```

---

## FhirView Column Creation

### Description
Methods within `FhirView` to create `Column` objects.

### Methods

#### `static Column` column(String name, String path)
Creates a new `Column` with the specified name and path.

### Request Example
```json
{
  "example": "FhirView.column('myColumn', 'path.to.column')"
}
```

### Response
#### Success Response (200)
- **Column** (object) - A representation of the created Column.

#### Response Example
```json
{
  "example": "Column representation"
}
```
```

--------------------------------

### Check Spark Installation in R

Source: https://pathling.csiro.au/docs/r/reference/pathling_is_spark_installed

The `pathling_is_spark_installed()` function checks if the Spark/Hadoop version required by the Pathling package is installed on the system. It returns TRUE if the installation is detected and FALSE otherwise. This function has no direct input parameters.

```r
pathling_is_spark_installed()
```

--------------------------------

### AnsiSqlToSparkDataTypeVisitor Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/views/ansi/AnsiSqlToSparkDataTypeVisitor

Initializes a new instance of the AnsiSqlToSparkDataTypeVisitor class.

```APIDOC
## AnsiSqlToSparkDataTypeVisitor Constructor

### Description
Constructs a new AnsiSqlToSparkDataTypeVisitor.

### Method
`public` AnsiSqlToSparkDataTypeVisitor()

### Parameters
None

### Request Example
```java
AnsiSqlToSparkDataTypeVisitor visitor = new AnsiSqlToSparkDataTypeVisitor();
```

### Response
(Constructor does not return a value)

### Response Example
N/A
```

--------------------------------

### Get Unit Code (Java)

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/FhirPathQuantity

Gets the canonical code for this quantity's unit.

```java
@Nonnull public String getCode()
```

--------------------------------

### ResourceCollection Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/collection/ResourceCollection

Details on how to create a new ResourceCollection instance.

```APIDOC
## ResourceCollection Constructor

### Description
Creates a new ResourceCollection.

### Method
`protected ResourceCollection(@Nonnull ColumnRepresentation columnRepresentation, @Nonnull Optional<FhirPathType> type, @Nonnull Optional<Enumerations.FHIRDefinedType> fhirType, @Nonnull Optional<? extends NodeDefinition> definition, @Nonnull ResourceDefinition resourceDefinition)`

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (N/A)
This is a constructor, not an endpoint that returns data.

#### Response Example
None
```

--------------------------------

### Get System URI (Java)

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/FhirPathQuantity

Gets the system URI for this quantity's unit.

```java
@Nonnull public String getSystem()
```

--------------------------------

### DataSinkBuilder Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/library/io/sink/DataSinkBuilder

Initializes a new DataSinkBuilder with a Pathling context and data source.

```APIDOC
## DataSinkBuilder Constructor

### Description
Initializes a new DataSinkBuilder with a Pathling context and data source.

### Method
CONSTRUCTOR

### Endpoint
N/A

### Parameters
#### Path Parameters
N/A

#### Query Parameters
N/A

#### Request Body
N/A

### Request Example
N/A

### Response
#### Success Response (N/A)
N/A

#### Response Example
N/A
```

--------------------------------

### Configure Pathling Pre-release Version in Java

Source: https://pathling.csiro.au/docs/libraries/installation/prerelease

Sets up a SparkSession in Java to integrate with a pre-release version of the Pathling library. It configures Spark to find the library from the snapshot repository. Requires Java Development Kit, Apache Spark, and Pathling libraries.

```java
import au.csiro.pathling.library.PathlingContext;
import org.apache.spark.sql.SparkSession;

class MyApp {

    public static void main(String[] args) {
        SparkSession spark = SparkSession.builder()
                .config("spark.jars.packages",  
                        "au.csiro.pathling:library-runtime:[some pre-release version]-SNAPSHOT")
                .config("spark.jars.repositories",  
                        "https://central.sonatype.com/repository/maven-snapshots")
                .getOrCreate();
        PathlingContext pc = PathlingContext.create(spark);
    }
}
```

--------------------------------

### ColumnSelection Constructor and Methods

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/projection/ColumnSelection

This section details the constructor and key methods of the ColumnSelection record, including how to create a selection and evaluate it.

```APIDOC
## ColumnSelection API

### Description
Represents a column selection for creating a projection from requested columns.

### Constructor
#### `ColumnSelection(List<RequestedColumn> columns)`
Creates an instance of a `ColumnSelection` record class.

**Parameters**:
- `columns` (List<RequestedColumn>) - Required - The list of columns to include in the projection.

### Methods
#### `evaluate(ProjectionContext context)`
Converts this clause into a result using the supplied context.

**Parameters**:
- `context` (ProjectionContext) - Required - The context in which to evaluate this clause.

**Returns**:
- `ProjectionResult` - The result of evaluating this clause.

#### `toExpression()`
Returns a string expression representation of this column selection.

**Returns**:
- `String` - The string expression "columns".

#### `columns()`
Returns the value of the `columns` record component.

**Returns**:
- `List<RequestedColumn>` - The value of the `columns` record component.

#### `toString()`
Returns a string representation of this record class.

**Returns**:
- `String` - A string representation of this object.

#### `hashCode()`
Returns a hash code value for this object.

**Returns**:
- `int` - A hash code value for this object.

#### `equals(Object o)`
Indicates whether some other object is "equal to" this one.

**Parameters**:
- `o` (Object) - Required - The object with which to compare.

**Returns**:
- `boolean` - `true` if this object is the same as the `o` argument; `false` otherwise.

### Example Usage
```java
import au.csiro.pathling.projection.ColumnSelection;
import au.csiro.pathling.projection.RequestedColumn;
import au.csiro.pathling.projection.ProjectionContext;
import au.csiro.pathling.projection.ProjectionResult;

import java.util.List;

// Assuming you have a list of RequestedColumn objects and a ProjectionContext
List<RequestedColumn> requestedColumns = ...;
ProjectionContext projectionContext = ...;

// Create a ColumnSelection
ColumnSelection columnSelection = new ColumnSelection(requestedColumns);

// Evaluate the selection
ProjectionResult result = columnSelection.evaluate(projectionContext);

// Get the expression string
String expression = columnSelection.toExpression();

// Get the list of columns
List<RequestedColumn> columns = columnSelection.columns();
```
```

--------------------------------

### FHIR Data Encoding and Examples

Source: https://pathling.csiro.au/docs/r/reference/index

Functions for encoding FHIR data into dataframes and accessing example data.

```APIDOC
## FHIR Data Encoding and Examples

### Description
This section describes functions for encoding FHIR resources (JSON or XML) into Spark DataFrames and accessing example FHIR data provided by Pathling.

### Functions

- **`pathling_encode(fhir_data)`**
  - **Description**: Encode FHIR JSON or XML to a dataframe.
  - **Method**: Not applicable (function)
  - **Endpoint**: Not applicable (function)

- **`pathling_encode_bundle(fhir_bundle)`**
  - **Description**: Encode FHIR Bundles to a dataframe.
  - **Method**: Not applicable (function)
  - **Endpoint**: Not applicable (function)

- **`pathling_example_resource(resource_name)`**
  - **Description**: Read resource from Pathling example data.
  - **Method**: Not applicable (function)
  - **Endpoint**: Not applicable (function)

- **`pathling_examples()`**
  - **Description**: Get path to Pathling example data.
  - **Method**: Not applicable (function)
  - **Endpoint**: Not applicable (function)
```

--------------------------------

### Java BuiltInConstantResolver Constructor and Get Method

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/variable/BuiltInConstantResolver

This snippet shows the constructor and the 'get' method of the BuiltInConstantResolver class. The constructor initializes the resolver, and the 'get' method retrieves an environment variable by its name, returning an Optional collection if found.

```java
public BuiltInConstantResolver() {
    // Constructor implementation
}

public Optional<Collection> get(@Nonnull String name) {
    // Method implementation to get a variable by name
    return Optional.empty(); // Placeholder for actual implementation
}
```

--------------------------------

### Install Devtools R Package

Source: https://pathling.csiro.au/docs/r/index

Installs the 'devtools' R package from the CRAN repository using Rscript.

```shell
Rscript --vanilla -e 'install.packages("devtools", repos="https://cloud.r-project.org/")'
```

--------------------------------

### SubsumesUdf Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/terminology/class-use/TerminologyServiceFactory

Explains how to create a `SubsumesUdf` instance with a `TerminologyServiceFactory`.

```APIDOC
## SubsumesUdf constructor

### Description
Creates a new `SubsumesUdf` with the specified `TerminologyServiceFactory`.

### Method
`SubsumesUdf`

### Endpoint
N/A (Java constructor)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```java
SubsumesUdf subsumesUdf = new SubsumesUdf(terminologyServiceFactory);
```

### Response
#### Success Response (200)
- **SubsumesUdf** (object) - A new instance of SubsumesUdf.

#### Response Example
```json
{
  "example": "SubsumesUdf object"
}
```
```

--------------------------------

### Aggregate Operation - GET

Source: https://pathling.csiro.au/docs/7.2.0/server/operations/aggregate

Perform aggregate queries using the GET method. Specify aggregation, grouping, and filter expressions in the URL parameters.

```APIDOC
## GET [FHIR endpoint]/[resource type]/$aggregate

### Description
Perform aggregate queries on FHIR server data using GET requests. This endpoint allows for specifying aggregation, grouping, and filter expressions in the URL.

### Method
GET

### Endpoint
`[FHIR endpoint]/[resource type]/$aggregate`

### Query Parameters
- **aggregation** (string) - Required (1..*) - A FHIRPath expression to calculate summary values for each grouping. Must return a materializable and singular type.
- **grouping** (string) - Optional (0..*) - A FHIRPath expression to determine the groupings for each resource. Must return a materializable type.
- **filter** (string) - Optional (0..*) - A FHIRPath expression to filter resources. Must evaluate to a Boolean. Multiple filters are combined with AND logic.

### Response
#### Success Response (200)
Returns a Parameters resource containing grouped results.
- **grouping** (array) - Contains the grouped results based on the query. Each element represents a distinct combination of grouping values.
  - **label** (array) - Descriptive labels for the grouping, corresponding to the query's grouping expressions.
  - **result** (array) - Aggregated values, corresponding to the query's aggregation expressions.
  - **drillDown** (string) - Optional - A FHIRPath expression to retrieve the resources belonging to this grouping (omitted if no groupings or filters were used).

#### Response Example
```json
{
  "resourceType": "Parameters",
  "parameter": [
    {
      "name": "grouping",
      "part": [
        {
          "name": "label",
          "valueString": "Example Label"
        },
        {
          "name": "result",
          "valueDecimal": 100
        },
        {
          "name": "drillDown",
          "valueString": "Observation?code=http://loinc.org|29552-2"
        }
      ]
    }
  ]
}
```
```

--------------------------------

### PathlingContext Initialization Configuration

Source: https://pathling.csiro.au/docs/python/pathling

Configuration options for initializing a PathlingContext. These parameters allow fine-grained control over caching, authentication, network requests, and debugging.

```APIDOC
## PathlingContext Initialization Configuration

### Description
Configuration parameters for initializing a `PathlingContext`.

### Parameters
#### PathlingContext Configuration Parameters
- **cache_storage_path** (string) - Required - The path on disk to use for the cache, required when `cache_storage_type` is 'disk'.
- **cache_default_expiry** (integer) - Optional - The default expiry time for cache entries (in seconds), used when the server does not provide an expiry value.
- **cache_override_expiry** (integer) - Optional - If provided, this value overrides the expiry time provided by the terminology server.
- **enable_auth** (boolean) - Optional - Enables authentication of requests to the terminology server.
- **token_endpoint** (string) - Optional - An OAuth2 token endpoint for use with the client credentials grant.
- **client_id** (string) - Optional - A client ID for use with the client credentials grant.
- **client_secret** (string) - Optional - A client secret for use with the client credentials grant.
- **scope** (string) - Optional - A scope value for use with the client credentials grant.
- **token_expiry_tolerance** (integer) - Optional - The minimum number of seconds that a token should have before expiry when deciding whether to send it with a terminology request.
- **accept_language** (string) - Optional - The default value of the Accept-Language HTTP header passed to the terminology server. The value may contain multiple languages, with weighted preferences as defined in https://www.rfc-editor.org/rfc/rfc9110.html#name-accept-language. If not provided, the header is not sent.
- **explain_queries** (boolean) - Optional - Setting this option to `True` will enable additional logging relating to the query plan used to execute queries.
- **max_unbound_traversal_depth** (integer) - Optional - Maximum depth for self-referencing structure traversals in repeat operations. Controls how deeply nested hierarchical data can be flattened during projection.
- **enable_delta** (boolean) - Optional - Enables the use of Delta for storage of FHIR data. Only supported when no SparkSession is provided.
- **enable_remote_debugging** (boolean) - Optional - Enables remote debugging for the JVM process.
- **debug_port** (integer) - Optional - The port for the debugger to listen on (default: 5005).
- **debug_suspend** (boolean) - Optional - If true, the JVM will suspend until a debugger is attached.
```

--------------------------------

### GET /resource type?_query=fhirPath&filter=[FHIRPath expression]

Source: https://pathling.csiro.au/docs/7.2.0/server/operations/search

Retrieves FHIR resources filtered by one or more FHIRPath expressions using a GET request.

```APIDOC
## GET [FHIR endpoint]/[resource type]?_query=fhirPath&filter=[FHIRPath expression]

### Description
This endpoint allows you to retrieve a set of FHIR resources from the server filtered by one or more FHIRPath expressions. Each expression is evaluated against each resource, returning a Boolean value which determines whether the resource will be included in the search result.

### Method
GET

### Endpoint
`[FHIR endpoint]/[resource type]`

### Parameters
#### Query Parameters
- **_query** (string) - Required - Must be set to `fhirPath` to invoke the FHIRPath search.
- **filter** (string) - Required (1..*) - A FHIRPath expression that can be evaluated against each resource in the data set to determine whether it is included within the result. The context is an individual resource of the type that the search is being invoked against. The expression must evaluate to a Boolean value. Multiple filter expressions can be provided and delimited by commas for OR logic.
- **_count** (integer) - Optional - Specifies the number of resources to return in a single response. Defaults to 100.

### Request Example
```
GET https://example.fhir.com/Patient?_query=fhirPath&filter=gender%3Dmale
```

### Response
#### Success Response (200)
Returns a FHIR Bundle containing matching resources. The bundle may include pagination links if a large number of resources are returned.

#### Response Example
```json
{
  "resourceType": "Bundle",
  "total": 2,
  "entry": [
    {
      "fullUrl": "https://example.fhir.com/Patient/123",
      "resource": {
        "resourceType": "Patient",
        "id": "123",
        "gender": "male"
      }
    },
    {
      "fullUrl": "https://example.fhir.com/Patient/456",
      "resource": {
        "resourceType": "Patient",
        "id": "456",
        "gender": "male"
      }
    }
  ]
}
```
```

--------------------------------

### PathlingContext Creation

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/terminology/class-use/TerminologyServiceFactory

Demonstrates how to create a PathlingContext using the TerminologyServiceFactory for advanced testing configurations.

```APIDOC
## PathlingContext.createInternal

### Description
Creates a `PathlingContext` with advanced configuration for testing purposes, utilizing a provided `TerminologyServiceFactory`.

### Method
`static PathlingContext`

### Endpoint
N/A (Java method)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```java
PathlingContext context = PathlingContext.createInternal(spark, fhirEncoders, terminologyServiceFactory);
```

### Response
#### Success Response (200)
- **PathlingContext** (object) - An instance of PathlingContext configured for testing.

#### Response Example
```json
{
  "example": "PathlingContext object"
}
```
```

--------------------------------

### Install R using Miniconda

Source: https://pathling.csiro.au/docs/r/index

Installs R version 4.1.3 using Conda within an activated development environment, managed by Miniconda.

```shell
# run 'conda activate your-dev-env-name' first
conda install -y -c conda-forge r-base=4.1.3
```

--------------------------------

### UrlDownloadEntry Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/fhir/export/download/UrlDownloadTemplate.UrlDownloadEntry

This section details the constructor for the UrlDownloadEntry class. It is used to create a new instance of a URL download entry.

```APIDOC
## POST /websites/pathling_csiro_au/UrlDownloadEntry

### Description
Creates a new instance of a URL download entry.

### Method
POST

### Endpoint
/websites/pathling_csiro_au/UrlDownloadEntry

### Parameters
#### Query Parameters
None

#### Request Body
None

### Request Example
```json
{
  "example": "No request body required for default constructor."
}
```

### Response
#### Success Response (201)
- **message** (string) - Indicates successful creation of the UrlDownloadEntry.

#### Response Example
```json
{
  "message": "UrlDownloadEntry created successfully."
}
```
```

--------------------------------

### build (no definition)

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/collection/CodingCollection

Returns a new instance of CodingCollection with the specified column and no definition.

```APIDOC
## POST /api/coding/build/noDefinition

### Description
Returns a new instance of CodingCollection with the specified column and no definition.

### Method
`public static CodingCollection build`

### Parameters
#### Request Body
- **columnRepresentation** (ColumnRepresentation) - Required - The column to use.

### Request Example
```json
{
  "columnRepresentation": "exampleColumn"
}
```

### Response
#### Success Response (200)
- **CodingCollection** (CodingCollection) - A new instance of `CodingCollection`.

#### Response Example
```json
{
  "message": "CodingCollection built successfully"
}
```
```

--------------------------------

### Install Pathling Helm Chart

Source: https://pathling.csiro.au/docs/7.2.0/server/kubernetes

Commands to add the Pathling Helm repository, update chart information, and install the Pathling server chart.

```shell
# Add the Pathling Helm repository.  
helm repo add pathling https://pathling.csiro.au/helm  
  
# Get the latest information about charts from the repository.  
helm repo update  
  
# Install the Pathling server chart as a release named `pathling`, with the   
# default values.  
helm install pathling pathling/pathling  

```

--------------------------------

### AnsiSqlToSparkDataTypeVisitor Constructor

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/views/ansi/AnsiSqlToSparkDataTypeVisitor

Initializes an instance of the AnsiSqlToSparkDataTypeVisitor. This is a default constructor with no parameters, setting up the visitor for traversal.

```java
public AnsiSqlToSparkDataTypeVisitor()
Constructor.
```

--------------------------------

### Install Pathling R Package and Spark

Source: https://pathling.csiro.au/docs/r/index

Installs the 'pathling' R package and the Spark version required by Pathling. Ensure R version is 3.5.0 or higher.

```r
# Install the `pathling` package.
install.packages('pathling')

# Install the Spark version required by Pathling.
pathling::pathling_install_spark()
```

--------------------------------

### Build HTTP Client Configuration

Source: https://pathling.csiro.au/docs/python/_modules/pathling/context

Creates an `HttpClientConfiguration` for terminology services. This configuration includes settings for socket timeout, connection pooling, and retry behavior.

```python
jvm.au.csiro.pathling.config.HttpClientConfiguration.builder()
            .socketTimeout(terminology_socket_timeout)
            .maxConnectionsTotal(max_connections_total)
            .maxConnectionsPerRoute(max_connections_per_route)
            .retryEnabled(terminology_retry_enabled)
            .retryCount(terminology_retry_count)
            .build()
```

--------------------------------

### Get Pathling Version (R)

Source: https://pathling.csiro.au/docs/r/reference/pathling_version

This function returns the version of the Pathling R library. It has no dependencies and takes no arguments. The output is a string representing the library version.

```r
pathling_version()
```

--------------------------------

### Build Terminology Configuration

Source: https://pathling.csiro.au/docs/python/_modules/pathling/context

Assembles a complete `TerminologyConfiguration` by integrating client, cache, and authentication configurations. It also includes settings for server URL, verbose logging, and accept language.

```python
terminology_config = (
            jvm.au.csiro.pathling.config.TerminologyConfiguration.builder()
            .enabled(enable_terminology)
            .serverUrl(terminology_server_url)
            .verboseLogging(terminology_verbose_request_logging)
            .client(client_config)
            .cache(cache_config)
            .authentication(auth_config)
            .acceptLanguage(accept_language)
            .build()
```

--------------------------------

### Get Environment Variable by Name - Java

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/variable/Hl7ExtensionResolver

Retrieves an environment variable by its name. This method is part of the EnvironmentVariableResolver interface and is implemented to get FHIR-specific environment variables.

```java
public Optional<Collection> get(@Nonnull String name)
```

--------------------------------

### Install Development Dependencies for Devtools on MacOS

Source: https://pathling.csiro.au/docs/r/index

Installs additional Homebrew packages required for building 'devtools' dependencies, including harfbuzz, fribidi, libjpeg, libtiff, and libgit2.

```shell
brew install harfbuzz fribidi
brew install libjpeg
brew install libtiff
brew install libgit2
```

--------------------------------

### read

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/library/PathlingContext

Initializes a DataSourceBuilder for reading data from various sources.

```APIDOC
## GET /read

### Description
Returns a new `DataSourceBuilder` that can be used to read from a variety of different data sources.

### Method
GET

### Endpoint
/read

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
- **DataSourceBuilder** (object) - A new instance of DataSourceBuilder.

#### Response Example
```json
{
  "message": "DataSourceBuilder initialized"
}
```
```

--------------------------------

### ResourceCollection Build Methods

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/collection/ResourceCollection

Static methods for building ResourceCollection instances.

```APIDOC
## ResourceCollection Build Methods

### Description
Provides static methods to construct `ResourceCollection` objects.

### Method
`@Nonnull public static ResourceCollection build(@Nonnull ColumnRepresentation columnRepresentation, @Nonnull ResourceDefinition definition)`

#### Parameters
*   **columnRepresentation** (ColumnRepresentation) - Required - The column representation to use.
*   **definition** (ResourceDefinition) - Required - The resource definition.

### Method
`@Nonnull public static ResourceCollection build(@Nonnull ColumnRepresentation columnRepresentation, @Nonnull FhirContext fhirContext, @Nonnull Enumerations.ResourceType resourceType)`

#### Parameters
*   **columnRepresentation** (ColumnRepresentation) - Required - A column representation to use for the resource.
*   **fhirContext** (FhirContext) - Required - The `FhirContext` to use for sourcing the resource definition.
*   **resourceType** (Enumerations.ResourceType) - Required - The type of the resource.

### Request Example
None

### Response
#### Success Response (200)
*   **ResourceCollection** (ResourceCollection) - A new `ResourceCollection` instance.
```

--------------------------------

### Build Query Configuration

Source: https://pathling.csiro.au/docs/python/_modules/pathling/context

Creates a `QueryConfiguration` object for query execution. This configuration controls query explanation and the maximum depth for unbound traversals.

```python
jvm.au.csiro.pathling.config.QueryConfiguration.builder()
            .explainQueries(explain_queries)
            .maxUnboundTraversalDepth(max_unbound_traversal_depth)
            .build()
```

--------------------------------

### PathlingContext Builder Methods

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/library/class-use/PathlingContext.Builder

This section details the methods available on the PathlingContext.Builder class for creating and configuring a PathlingContext.

```APIDOC
## PathlingContext.Builder

### Description
Provides methods for creating and configuring a `PathlingContext`.

### Methods

#### `builder()`

*   **Description**: Creates a new `PathlingContext.Builder` for building a `PathlingContext`.
*   **Method**: `static PathlingContext.Builder`
*   **Endpoint**: N/A (Class method)

#### `builder(SparkSession spark)`

*   **Description**: Creates a new `PathlingContext.Builder` for building a `PathlingContext` with a pre-configured Spark session.
*   **Method**: `static PathlingContext.Builder`
*   **Parameters**:
    *   **spark** (`SparkSession`) - Required - The pre-configured Spark session.
*   **Endpoint**: N/A (Class method)

#### `encodingConfiguration(EncodingConfiguration encodingConfiguration)`

*   **Description**: Sets the encoding configuration for the context.
*   **Method**: `PathlingContext.Builder`
*   **Parameters**:
    *   **encodingConfiguration** (`EncodingConfiguration`) - Required - The encoding configuration to set.
*   **Endpoint**: N/A (Instance method)

#### `queryConfiguration(QueryConfiguration queryConfiguration)`

*   **Description**: Sets the query configuration for the context.
*   **Method**: `PathlingContext.Builder`
*   **Parameters**:
    *   **queryConfiguration** (`QueryConfiguration`) - Required - The query configuration to set.
*   **Endpoint**: N/A (Instance method)

#### `spark(SparkSession spark)`

*   **Description**: Sets the Spark session for the context.
*   **Method**: `PathlingContext.Builder`
*   **Parameters**:
    *   **spark** (`SparkSession`) - Required - The Spark session to set.
*   **Endpoint**: N/A (Instance method)

#### `terminologyConfiguration(TerminologyConfiguration terminologyConfiguration)`

*   **Description**: Sets the terminology configuration for the context.
*   **Method**: `PathlingContext.Builder`
*   **Parameters**:
    *   **terminologyConfiguration** (`TerminologyConfiguration`) - Required - The terminology configuration to set.
*   **Endpoint**: N/A (Instance method)

### Request Example
```json
{
  "example": "// Example of building a PathlingContext with custom configurations"
}
```

### Response
#### Success Response (200)
*   **PathlingContext** (`PathlingContext`) - The constructed PathlingContext object.

#### Response Example
```json
{
  "example": "// PathlingContext object is returned upon successful build."
}
```
```

--------------------------------

### getDisplayExpression

Source: https://pathling.csiro.au/docs/java/au/csiro/pathling/fhirpath/collection/Collection

Gets a user-friendly string representation of the collection.

```APIDOC
## getDisplayExpression

### Description
Gets a user-friendly representation of the current collection that can be used to refer to it in user errors.

### Method
`getDisplayExpression`

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
- **result** (`String`) - a user-friendly representation of the collection.

#### Response Example
```json
{
  "result": "User-friendly collection name"
}
```
```
Tokens:
Raw