pathling 9.2.0.dev1__tar.gz → 9.3.0__tar.gz

{pathling-9.2.0.dev1 → pathling-9.3.0}/LICENSE

@@ -183,11 +183,12 @@ agree to comply with the licence terms for these components as part of
 accessing the Software. Other third party software may also be identified in
 separate files distributed with the Software.
 
-* (Apache License, Version 2.0) FHIR Bulk Client (au.csiro.fhir:bulk-export:1.0.3 - https://github.com/aehrc/fhir-bulk-java)
+* (Apache License, Version 2.0) FHIR Bulk Client (au.csiro.fhir:bulk-export:1.0.4 - https://github.com/aehrc/fhir-bulk-java)
+* (Apache License, Version 2.0) FHIR Auth Client for Java (au.csiro.fhir:fhir-auth:1.0.0 - https://github.com/aehrc/fhir-auth-java)
 * (Apache License, Version 2.0) HAPI FHIR - Core Library (ca.uhn.hapi.fhir:hapi-fhir-base:8.6.0 - https://hapifhir.io/)
 * (Apache License, Version 2.0) HAPI FHIR - Client Framework (ca.uhn.hapi.fhir:hapi-fhir-client:8.6.0 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-client)
 * (Apache License, Version 2.0) HAPI FHIR Structures - FHIR R4 (ca.uhn.hapi.fhir:hapi-fhir-structures-r4:8.6.0 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-structures-r4)
-* (Eclipse Public License 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.18 - http://logback.qos.ch/logback-classic)
+* (Eclipse Public License 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.25 - http://logback.qos.ch/logback-classic)
 * (Apache License, Version 2.0) WireMock (com.github.tomakehurst:wiremock-jre8-standalone:2.35.2 - http://wiremock.org)
 * (Apache License, Version 2.0) FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.2 - http://findbugs.sourceforge.net/)
 * (Apache License, Version 2.0) Gson (com.google.code.gson:gson:2.10 - https://github.com/google/gson/gson)
@@ -203,16 +204,17 @@ separate files distributed with the Software.
 * (Apache License, Version 2.0) Apache Commons Lang (org.apache.commons:commons-lang3:3.18.0 - https://commons.apache.org/proper/commons-lang/)
 * (Apache License, Version 2.0) Apache Derby Tools (org.apache.derby:derbytools:10.16.1.1 - http://db.apache.org/derby/)
 * (Apache License, Version 2.0) Apache Hadoop Client API (org.apache.hadoop:hadoop-client-api:3.4.1 - no url defined)
-* (Apache License, Version 2.0) Spark Project Catalyst (org.apache.spark:spark-catalyst_2.13:4.0.1 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Core (org.apache.spark:spark-core_2.13:4.0.1 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Hive (org.apache.spark:spark-hive_2.13:4.0.1 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project SQL (org.apache.spark:spark-sql_2.13:4.0.1 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Unsafe (org.apache.spark:spark-unsafe_2.13:4.0.1 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Catalyst (org.apache.spark:spark-catalyst_2.13:4.0.2 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Core (org.apache.spark:spark-core_2.13:4.0.2 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Hive (org.apache.spark:spark-hive_2.13:4.0.2 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project SQL (org.apache.spark:spark-sql_2.13:4.0.2 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Unsafe (org.apache.spark:spark-unsafe_2.13:4.0.2 - https://spark.apache.org/)
 * (Apache License, Version 2.0) Awaitility (org.awaitility:awaitility:4.2.0 - http://awaitility.org)
 * (Apache License, Version 2.0) Hibernate Validator Engine (org.hibernate.validator:hibernate-validator:8.0.1.Final - http://hibernate.org/validator/hibernate-validator)
 * (Apache License, Version 2.0) Infinispan Commons (org.infinispan:infinispan-commons:15.0.3.Final - http://www.infinispan.org)
 * (Apache License, Version 2.0) Infinispan Component Annotations (org.infinispan:infinispan-component-annotations:15.0.3.Final - http://www.infinispan.org)
 * (Apache License, Version 2.0) Infinispan Core (org.infinispan:infinispan-core:15.0.3.Final - http://www.infinispan.org)
+* (Public Domain) JSON in Java (org.json:json:20231013 - https://github.com/douglascrockford/JSON-java)
 * (Public Domain) JSON in Java (org.json:json:20240303 - https://github.com/douglascrockford/JSON-java)
 * (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.11.4 - https://junit.org/junit5/)
 * (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.11.4 - https://junit.org/junit5/)
@@ -221,7 +223,8 @@ separate files distributed with the Software.
 * (GNU General Public License (GPL), version 2, with the Classpath exception) JMH Core (org.openjdk.jmh:jmh-core:1.37 - http://openjdk.java.net/projects/code-tools/jmh/jmh-core/)
 * (GNU General Public License (GPL), version 2, with the Classpath exception) JMH Generators: Annotation Processors (org.openjdk.jmh:jmh-generator-annprocess:1.37 - http://openjdk.java.net/projects/code-tools/jmh/jmh-generator-annprocess/)
 * (MIT License) Project Lombok (org.projectlombok:lombok:1.18.38 - https://projectlombok.org)
-* (Apache License, Version 2.0) Scala Library (org.scala-lang:scala-library:2.13.15 - https://www.scala-lang.org/)
+* (Apache License, Version 2.0) Scala Library (org.scala-lang:scala-library:2.13.16 - https://www.scala-lang.org/)
 * (Apache License, Version 2.0) JSONassert (org.skyscreamer:jsonassert:1.5.1 - https://github.com/skyscreamer/JSONassert)
+* (Apache License, Version 2.0) JSONassert (org.skyscreamer:jsonassert:1.5.3 - https://github.com/skyscreamer/JSONassert)
 * (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.17 - http://www.slf4j.org)
 * (Apache License, Version 2.0) spring-boot-starter-test (org.springframework.boot:spring-boot-starter-test:3.4.11 - https://spring.io/projects/spring-boot)

{pathling-9.2.0.dev1 → pathling-9.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pathling
-Version: 9.2.0.dev1
+Version: 9.3.0
 Summary: Python API for Pathling
 Project-URL: Homepage, https://github.com/aehrc/pathling
 Author-email: "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>

pathling-9.3.0/examples/fhir_search.py

@@ -0,0 +1,30 @@
+#  Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
+#  Organisation (CSIRO) ABN 41 687 119 230.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+import os
+
+from pathling import PathlingContext
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+DATA_DIR = os.path.join(HERE, "data")
+NDJSON_DIR = os.path.join(DATA_DIR, "resources")
+
+pc = PathlingContext.create()
+datasource = pc.read.ndjson(NDJSON_DIR)
+
+search_filter = pc.search_to_column("Patient", "gender=male&family=MacGyver")
+datasource.read("Patient").filter(search_filter).select(
+    "id", "gender", "name.family"
+).show()

{pathling-9.2.0.dev1 → pathling-9.3.0}/pathling/_version.py

@@ -2,8 +2,8 @@
 # Auto generated from POM project version.
 # Please do not modify.
 #
-__version__="9.2.0.dev1"
-__java_version__="9.2.0-SNAPSHOT"
+__version__="9.3.0"
+__java_version__="9.3.0"
 __scala_version__="2.13"
 __delta_version__="4.0.0"
 __hadoop_version__="3.4.1"

{pathling-9.2.0.dev1 → pathling-9.3.0}/pathling/context.py

@@ -18,7 +18,7 @@
 from typing import TYPE_CHECKING, Optional, Sequence
 
 from py4j.java_gateway import JavaObject
-from pyspark.sql import DataFrame, SparkSession
+from pyspark.sql import Column, DataFrame, SparkSession
 
 from pathling._version import (
     __delta_version__,
@@ -380,3 +380,72 @@ class PathlingContext:
         from pathling.datasource import DataSources
 
         return DataSources(self)
+
+    def fhirpath_to_column(
+        self, resource_type: str, fhirpath_expression: str
+    ) -> Column:
+        """
+        Converts a FHIRPath expression to a PySpark Column.
+
+        This method takes a FHIRPath expression and returns a PySpark Column that
+        can be used in DataFrame operations such as ``filter()`` and ``select()``.
+        Boolean expressions can be used for filtering, while other expressions can
+        be used for value extraction.
+
+        The expression should evaluate to a single value per resource row.
+
+        Example usage::
+
+            pc = PathlingContext.create(spark)
+
+            # Boolean expression for filtering
+            gender_filter = pc.fhirpath_to_column("Patient", "gender = 'male'")
+            filtered = patients.filter(gender_filter)
+
+            # Value expression for selection
+            name_col = pc.fhirpath_to_column("Patient", "name.given.first()")
+            names = patients.select(name_col)
+
+        :param resource_type: the FHIR resource type (e.g., "Patient", "Observation")
+        :param fhirpath_expression: the FHIRPath expression to evaluate
+        :return: a PySpark Column representing the evaluated expression
+        :raises: IllegalArgumentException if the resource type is invalid
+        :raises: Exception if the FHIRPath expression is invalid
+        """
+        jcolumn = self._jpc.fhirPathToColumn(resource_type, fhirpath_expression)
+        return Column(jcolumn)
+
+    def search_to_column(self, resource_type: str, search_expression: str) -> Column:
+        """
+        Converts a FHIR search expression to a boolean filter column.
+
+        This method takes a FHIR search query string and returns a PySpark Column
+        that can be used to filter a DataFrame of FHIR resources. The resulting
+        Column evaluates to true for resources that match the search criteria.
+
+        Example usage::
+
+            pc = PathlingContext.create(spark)
+
+            # Single parameter
+            gender_filter = pc.search_to_column("Patient", "gender=male")
+
+            # Multiple parameters (AND)
+            combined_filter = pc.search_to_column("Patient", "gender=male&birthdate=ge1990-01-01")
+
+            # Combine with Pythonic operators
+            filter1 = pc.search_to_column("Patient", "gender=male")
+            filter2 = pc.search_to_column("Patient", "active=true")
+            combined = filter1 & filter2
+
+            # Apply to DataFrame
+            patients = datasource.read("Patient")
+            filtered = patients.filter(combined)
+
+        :param resource_type: the FHIR resource type (e.g., "Patient", "Observation")
+        :param search_expression: URL query string format (e.g., "gender=male&birthdate=ge1990")
+        :return: a PySpark Column representing the boolean filter condition
+        :raises: IllegalArgumentException if the search expression contains unknown parameters
+        """
+        jcolumn = self._jpc.searchToColumn(resource_type, search_expression)
+        return Column(jcolumn)

{pathling-9.2.0.dev1 → pathling-9.3.0}/pyproject.toml

@@ -49,8 +49,8 @@ dev = [
     "sphinx-rtd-theme==1.2.2",
     "pytest==8.2.0",
     "ipython==8.10.0",
-    "wheel==0.43.0",
-    "twine==5.0.0",
+    "wheel==0.46.3",
+    "twine==6.2.0",
     "build==1.2.1",
     "pytest-cov==5.0.0",
     "http-server-mock==1.7",