pathling 8.0.0.dev0__tar.gz → 8.0.0.dev1__tar.gz

{pathling-8.0.0.dev0/pathling.egg-info → pathling-8.0.0.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pathling
-Version: 8.0.0.dev0
+Version: 8.0.0.dev1
 Summary: Python API for Pathling
 Home-page: https://github.com/aehrc/pathling
 Author: Australian e-Health Research Centre, CSIRO
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.10
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pyspark<3.6.0,>=3.5.0
+Requires-Dist: pyspark<3.6.0,>=3.5.2
 Requires-Dist: deprecated>=1.2.13
 Dynamic: author
 Dynamic: author-email
@@ -25,6 +25,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

pathling-8.0.0.dev1/examples/bulk.py

@@ -0,0 +1,151 @@
+#  Copyright 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
+import tempfile
+from datetime import datetime, timezone
+
+from pathling import PathlingContext
+
+jwk = """
+{
+  "kty": "RSA",
+  "alg": "RS384",
+  "n": "jcrw7Jio4RVAMlo2clxqkmT9nmg_w1pXhpChg0jp41fKKfDXAtlIRhL_Ij8_N71l5KVxNQWeNeGsO0op73Rj28HR885fxJ2jimYFyD0fsftjjHvYkV_GskFubhcURbHAvx3lVrwLFyILq8sydF2G48A-XSfVAHPE6yEimusRRNihPmbM-MDlBuQkLBtwnT0bDXUEIlpDvlPB30Im2QOgvYTsMAnI-MzemOAtF5Xe5wCsj27nityK5AlnAJLFXfeeFqySoIyR7FaaQ1eay40MV-ZyDULSPtV4C-58eh3V2SL-qkQEsfQSuu3rqb-lgOz1-gl4FqTIz2JGtpEsTM7Uww",
+  "e": "AQAB",
+  "d": "kwNFEgpaxeAeHTtrypSZoXjLM7u-YM3czV9w8huCrjSg1SSXgFykAJX6zT40BHJbMv8xhcgEQZBMub69vBqoAOirWPky5KiNMPG7VirlRDaGJSJDH-UJQzaUJCM3c-bYzQXpDE3rxBBkCXHJcJQabAkwDa8-4F26YFjWGqUMsFOE1sxTXPnJG8qBTYxTSFxnWNf6U_kbGOQlWtHd1TgxPjXzmU6H472igte6SZEATh9eyYgPJrAqnw4qRNGy5pnAHkuIrCHIMaktR34LKFHHl3_xsLSHo9QmPfEdR5soKIKQIph2KRYArx4U03larr7vbZMSOypLqBtoRVlzvx0h",
+  "p": "wmc-aV7SbViyP50B0s_6wrDlOjGid9kO7QePuohFLmJWuC8TP8VYeSBscCPf6gX40O8agiCrsBuz2ZUTZDlYBXPHRiYprdV11SgCXkfTw6-G5CD2Xjq43gcTzFOy2q2FlU5YtBkPVTrsYMH8p6F09sZRu-4rnCOpgoahbAawGXs",
+  "q": "urhDpiHoZj0SBjmfn8GTHNh3FoUE8xiG3s0e64xSIBE3PzXCmskZpJuKGqgPX-wSXer2_WtmJUzOCucajcd4HQp222PWMKhc1HVZMj4073XQKDGqe_M7ZH29RbS9x93zhNgvFFiSdubQTg9SHJXL3Ja0f3IYxReha13G9YDSG1k",
+  "dp": "thWN15QA9HpHOl4M_y_eZ8zYZ5Fl42tjF5Alh0lrwu5I22r8VJa7L3i3GLIBYGkHjGroIUoIhYLtCbcf2pf7Yd_3njTQhQmSvHwk-7m7F2aoqbRWDhxiW1O1r4QV2cz9ecNQQh_WxLXUASyxQTFxJFLM64FBR5X_h0oil9QLzVE",
+  "dq": "W_t8L_JSR1Ncdr6aWRwGOdaVS_25g3wYrNeFnOoiZvO0MKpuNMxOmp2Y-irCcDGelq-yfwMSbduZQRu6JBAYps3J4agcExpNqMgqaarlbvWt1q8o2ijnoEilHhq8xyIa3d2Vy8MaXAK2qU242KYeqIuBXas6cpWCip7G7ZhJaPk",
+  "qi": "bZvyduEpMUYyGXhd-MnHyKOiJtCUF_kbM0hUGr8AfJ6_bi8MEjBNMt5qZKGYYT6bXFJWiTTUFq6nZLmQJ7cY5lv57gAQOTlLy6hp-nqkNrH1P-5UAzEbUMhIdnPQcDEkBEjpfObHlwtrmaFFVKgpm5vqFFD-szMHPuZ43o0vS98",
+  "key_ops": [
+    "sign"
+  ],
+  "ext": true,
+  "kid": "b31ab1cd8db2c39287b3267a2914600c"
+}
+"""
+
+client_id = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCIsImtpZCI6InJlZ2lzdHJhdGlvbi10b2tlbiJ9.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.qI-820847HN1S37IGMVMKJRGeXQBrgbx91UZ7Av9djs"
+
+
+def test_bulk_exports():
+    # Initialize PathlingContext.
+    pc = PathlingContext.create()
+
+    # Base parameters from the demo server
+    fhir_server = "https://bulk-data.smarthealthit.org/eyJlcnIiOiIiLCJwYWdlIjoxMDAwMCwidGx0IjoxNSwibSI6MSwiZGVsIjowLCJzZWN1cmUiOjEsIm9wcCI6MTB9/fhir"
+    output_base = os.path.join(tempfile.gettempdir(), "bulk_export_test")
+    
+    if os.path.exists(output_base):
+        import shutil
+        shutil.rmtree(output_base)
+    os.makedirs(output_base)
+
+    # Test 1: System level export with all parameters.
+    print("\n=== Testing system level export with all parameters ===")
+    pc.read.bulk(
+        fhir_endpoint_url=fhir_server,
+        output_dir=f"{output_base}/system_detailed",
+        output_format="application/fhir+ndjson",
+        since=datetime(2015, 1, 1, tzinfo=timezone.utc),
+        types=["Patient", "Observation"],
+        elements=["id", "status"],
+        include_associated_data=["LatestProvenanceResources"],
+        type_filters=["Patient?status=active"],
+        output_extension="ndjson",
+        timeout=3600,
+        max_concurrent_downloads=5,
+        auth_config={
+            "enabled": True,
+            "client_id": client_id,
+            "private_key_jwk": jwk,
+            "token_endpoint": "https://bulk-data.smarthealthit.org/auth/token",
+            "use_smart": True,
+            "use_form_for_basic_auth": False,
+            "scope": "system/Patient.r system/Observation.r",
+            "token_expiry_tolerance": 120
+        }
+    )
+    print("System export completed successfully")
+
+    # Test 2: Group level export with minimal parameters.
+    print("\n=== Testing group level export with minimal parameters ===")
+    pc.read.bulk(
+        fhir_endpoint_url=fhir_server,
+        output_dir=f"{output_base}/group_basic",
+        group_id="BMCHealthNet"
+    )
+    print("Group export completed successfully")
+
+    # Test 3: Group level export with all parameters.
+    print("\n=== Testing group level export with all parameters ===")
+    pc.read.bulk(
+        fhir_endpoint_url=fhir_server,
+        output_dir=f"{output_base}/group_detailed",
+        group_id="BMCHealthNet",
+        output_format="application/fhir+ndjson",
+        since=datetime(2015, 1, 1, tzinfo=timezone.utc),
+        types=["Patient", "Condition", "Observation"],
+        elements=["id", "status"],
+        include_associated_data=["LatestProvenanceResources"],
+        type_filters=["Patient?status=active"],
+        output_extension="ndjson",
+        timeout=1800,
+        max_concurrent_downloads=8
+    )
+    print("Group export completed successfully")
+
+    # Test 4: Patient level export with minimal parameters.
+    print("\n=== Testing patient level export with minimal parameters ===")
+    pc.read.bulk(
+        fhir_endpoint_url=fhir_server,
+        output_dir=f"{output_base}/patient_basic",
+        patients=[
+            "Patient/58c297c4-d684-4677-8024-01131d93835e",
+            "Patient/118616a4-f0b2-411f-8050-39d5d27c738c"
+        ]
+    )
+    print("Patient export completed successfully")
+
+    # Test 5: Patient level export with all parameters.
+    print("\n=== Testing patient level export with all parameters ===")
+    pc.read.bulk(
+        fhir_endpoint_url=fhir_server,
+        output_dir=f"{output_base}/patient_detailed",
+        patients=[
+            "Patient/58c297c4-d684-4677-8024-01131d93835e",
+            "Patient/118616a4-f0b2-411f-8050-39d5d27c738c",
+            "Patient/21fba439-ca79-411f-a081-37a432a78f3a"
+        ],
+        output_format="application/fhir+ndjson",
+        since=datetime(2020, 1, 1, tzinfo=timezone.utc),
+        types=["Observation", "MedicationRequest"],
+        elements=["id", "status", "code"],
+        include_associated_data=["LatestProvenanceResources"],
+        type_filters=["Observation?category=vital-signs"],
+        output_extension="ndjson",
+        timeout=2400,
+        max_concurrent_downloads=3
+    )
+    print("Patient export completed successfully")
+
+    print("\nAll bulk exports completed successfully!")
+    print(f"Output written to: {output_base}")
+
+
+if __name__ == "__main__":
+    test_bulk_exports()

{pathling-8.0.0.dev0 → pathling-8.0.0.dev1}/pathling/__init__.py

@@ -19,7 +19,6 @@ from .core import Expression, VariableExpression
 from .datasource import DataSources, DataSource
 from .fhir import MimeType, Version
 from .functions import to_coding, to_snomed_coding, to_ecl_value_set
-from .query import ExtractQuery, AggregateQuery
 from .udfs import (
     member_of,
     translate,
@@ -52,8 +51,6 @@ __all__ = [
     "to_ecl_value_set",
     "Expression",
     "VariableExpression",
-    "ExtractQuery",
-    "AggregateQuery",
     "DataSources",
     "DataSource",
 ]

{pathling-8.0.0.dev0 → pathling-8.0.0.dev1}/pathling/_version.py

@@ -2,8 +2,8 @@
 # Auto generated from POM project version.
 # Please do not modify.
 #
-__version__="8.0.0.dev0"
+__version__="8.0.0.dev1"
 __java_version__="8.0.0-SNAPSHOT"
 __scala_version__="2.12"
-__delta_version__="3.2.0"
+__delta_version__="3.3.2"
 __hadoop_version__="3.3.4"

pathling-8.0.0.dev1/pathling/bulk.py

@@ -0,0 +1,234 @@
+#  Copyright 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.
+
+from datetime import datetime
+from typing import List, Optional
+
+from pathling import PathlingContext
+
+
+class BulkExportClient:
+    """
+    A client for exporting data from the FHIR Bulk Data Access API.
+    """
+    def __init__(self, java_client):
+        """
+        Create a new BulkExportClient that wraps a Java BulkExportClient.
+        
+        :param java_client: The Java BulkExportClient instance to wrap
+        """
+        self._java_client = java_client
+
+    def export(self):
+        """
+        Export data from the FHIR server.
+        
+        :return: The result of the export operation
+        """
+        return self._java_client.export()
+
+    @classmethod
+    def _configure_builder(cls, jvm, builder, fhir_endpoint_url: str, output_dir: str,
+                      output_format: str = "application/fhir+ndjson",
+                      since: Optional[datetime] = None,
+                      types: Optional[List[str]] = None, 
+                      elements: Optional[List[str]] = None,
+                      include_associated_data: Optional[List[str]] = None,
+                      type_filters: Optional[List[str]] = None,
+                      output_extension: str = "ndjson",
+                      timeout: Optional[int] = None,
+                      max_concurrent_downloads: int = 10,
+                      auth_config: Optional[dict] = None):
+        """
+        Configure common builder parameters.
+        
+        :param jvm: The JVM instance
+        :param builder: The builder instance to configure
+        :param fhir_endpoint_url: The URL of the FHIR server
+        :param output_dir: Output directory
+        :param output_format: Output format
+        :param since: Timestamp filter (must include timezone information)
+        :param types: Resource types to include
+        :param elements: Elements to include
+        :param include_associated_data: Associated data to include
+        :param type_filters: Resource filters
+        :param output_extension: File extension for output files
+        :param timeout: Optional timeout duration in seconds
+        :param max_concurrent_downloads: Maximum number of concurrent downloads
+        :param auth_config: Optional authentication configuration dictionary with the following possible keys:
+            - enabled: Whether authentication is enabled (default: False)
+            - client_id: The client ID to use for authentication
+            - private_key_jwk: The private key in JWK format
+            - client_secret: The client secret to use for authentication
+            - token_endpoint: The token endpoint URL
+            - use_smart: Whether to use SMART authentication (default: True)
+            - use_form_for_basic_auth: Whether to use form-based basic auth (default: False)
+            - scope: The scope to request
+            - token_expiry_tolerance: The token expiry tolerance in seconds (default: 120)
+        """
+        builder.withFhirEndpointUrl(fhir_endpoint_url)
+        builder.withOutputDir(output_dir)
+        builder.withOutputFormat(output_format)
+        builder.withOutputExtension(output_extension)
+        builder.withMaxConcurrentDownloads(max_concurrent_downloads)
+
+        if timeout is not None:
+            java_duration = jvm.java.time.Duration.ofSeconds(timeout)
+            builder.withTimeout(java_duration)
+
+        if since is not None:
+            if since.tzinfo is None:
+                raise ValueError("datetime must include timezone information")
+            # Format with microsecond precision and timezone offset
+            instant_str = since.strftime('%Y-%m-%dT%H:%M:%S.%f')[:-3]  # Truncate to milliseconds
+            if since.utcoffset() is None:
+                instant_str += 'Z'
+            else:
+                offset = since.strftime('%z')
+                # Insert colon in timezone offset
+                instant_str += f"{offset[:3]}:{offset[3:]}"
+            java_instant = jvm.java.time.Instant.parse(instant_str)
+            builder.withSince(java_instant)
+        if types is not None:
+            for type_ in types:
+                builder.withType(type_)
+        if elements is not None:
+            for element in elements:
+                builder.withElement(element)
+        if include_associated_data is not None:
+            # Convert Python list to Java List<String>
+            java_list = jvm.java.util.ArrayList()
+            for data in include_associated_data:
+                java_list.add(data)
+            builder.withIncludeAssociatedData(java_list)
+        if type_filters is not None:
+            for filter_ in type_filters:
+                builder.withTypeFilter(filter_)
+
+        if auth_config is not None:
+            auth_builder = jvm.au.csiro.fhir.auth.AuthConfig.builder()
+            
+            # Set defaults to match Java class
+            auth_builder.enabled(False)
+            auth_builder.useSMART(True)
+            auth_builder.useFormForBasicAuth(False)
+            auth_builder.tokenExpiryTolerance(120)
+
+            # Map Python config to Java builder methods
+            if 'enabled' in auth_config:
+                auth_builder.enabled(auth_config['enabled'])
+            if 'use_smart' in auth_config:
+                auth_builder.useSMART(auth_config['use_smart'])
+            if 'token_endpoint' in auth_config:
+                auth_builder.tokenEndpoint(auth_config['token_endpoint'])
+            if 'client_id' in auth_config:
+                auth_builder.clientId(auth_config['client_id'])
+            if 'client_secret' in auth_config:
+                auth_builder.clientSecret(auth_config['client_secret'])
+            if 'private_key_jwk' in auth_config:
+                auth_builder.privateKeyJWK(auth_config['private_key_jwk'])
+            if 'use_form_for_basic_auth' in auth_config:
+                auth_builder.useFormForBasicAuth(auth_config['use_form_for_basic_auth'])
+            if 'scope' in auth_config:
+                auth_builder.scope(auth_config['scope'])
+            if 'token_expiry_tolerance' in auth_config:
+                auth_builder.tokenExpiryTolerance(auth_config['token_expiry_tolerance'])
+
+            auth_config_obj = auth_builder.build()
+            builder.withAuthConfig(auth_config_obj)
+
+    @classmethod
+    def for_system(cls, jvm, *args, **kwargs) -> 'BulkExportClient':
+        """
+        Create a builder for a system-level export.
+        
+        :param jvm: The JVM instance
+        :param fhir_endpoint_url: The URL of the FHIR server to export from
+        :param output_dir: The directory to write the output files to
+        :param output_format: The format of the output data
+        :param since: Only include resources modified after this timestamp
+        :param types: List of FHIR resource types to include
+        :param elements: List of FHIR elements to include
+        :param include_associated_data: Pre-defined set of FHIR resources to include
+        :param type_filters: FHIR search queries to filter resources
+        :param output_extension: File extension for output files
+        :param timeout: Optional timeout duration in seconds
+        :param max_concurrent_downloads: Maximum number of concurrent downloads
+        :param auth_config: Optional authentication configuration dictionary
+        :return: A BulkExportClient configured for system-level export
+        """
+        client_class = jvm.au.csiro.fhir.export.BulkExportClient
+        builder = client_class.systemBuilder()  # Returns a builder directly
+        cls._configure_builder(jvm, builder, *args, **kwargs)
+        return cls(builder.build())
+
+    @classmethod  
+    def for_group(cls, jvm, fhir_endpoint_url: str, output_dir: str,
+                  group_id: str, *args, **kwargs) -> 'BulkExportClient':
+        """
+        Create a builder for a group-level export.
+        
+        :param jvm: The JVM instance
+        :param fhir_endpoint_url: The URL of the FHIR server to export from
+        :param output_dir: The directory to write the output files to
+        :param group_id: The ID of the group to export
+        :param output_format: The format of the output data
+        :param since: Only include resources modified after this timestamp
+        :param types: List of FHIR resource types to include
+        :param elements: List of FHIR elements to include
+        :param include_associated_data: Pre-defined set of FHIR resources to include
+        :param type_filters: FHIR search queries to filter resources
+        :param output_extension: File extension for output files
+        :param timeout: Optional timeout duration in seconds
+        :param max_concurrent_downloads: Maximum number of concurrent downloads
+        :param auth_config: Optional authentication configuration dictionary
+        :return: A BulkExportClient configured for group-level export
+        """
+        client_class = jvm.au.csiro.fhir.export.BulkExportClient
+        # Pass group_id directly to groupBuilder
+        builder = client_class.groupBuilder(group_id)
+        cls._configure_builder(jvm, builder, fhir_endpoint_url, output_dir, *args, **kwargs)
+        return cls(builder.build())
+
+    @classmethod
+    def for_patient(cls, jvm, fhir_endpoint_url: str, output_dir: str,
+                    patients: Optional[List[str]] = None, *args, **kwargs) -> 'BulkExportClient':
+        """
+        Create a builder for a patient-level export.
+        
+        :param jvm: The JVM instance
+        :param fhir_endpoint_url: The URL of the FHIR server to export from
+        :param output_dir: The directory to write the output files to
+        :param patients: List of patient references to include
+        :param output_format: The format of the output data
+        :param since: Only include resources modified after this timestamp
+        :param types: List of FHIR resource types to include
+        :param elements: List of FHIR elements to include
+        :param include_associated_data: Pre-defined set of FHIR resources to include
+        :param type_filters: FHIR search queries to filter resources
+        :param output_extension: File extension for output files
+        :param timeout: Optional timeout duration in seconds
+        :param max_concurrent_downloads: Maximum number of concurrent downloads
+        :param auth_config: Optional authentication configuration dictionary
+        :return: A BulkExportClient configured for patient-level export
+        """
+        client_class = jvm.au.csiro.fhir.export.BulkExportClient
+        builder = client_class.patientBuilder()  # Returns a builder directly
+        if patients is not None:
+            for patient in patients:
+                ref = jvm.au.csiro.fhir.model.Reference.of(patient)
+                builder.withPatient(ref)
+        cls._configure_builder(jvm, builder, fhir_endpoint_url, output_dir, *args, **kwargs)
+        return cls(builder.build())

{pathling-8.0.0.dev0 → pathling-8.0.0.dev1}/pathling/context.py

@@ -104,6 +104,9 @@ class PathlingContext:
         token_expiry_tolerance: Optional[int] = 120,
         accept_language: Optional[str] = None,
         enable_delta=False,
+        enable_remote_debugging: Optional[bool] = False,
+        debug_port: Optional[int] = 5005,
+        debug_suspend: Optional[bool] = True,
     ) -> "PathlingContext":
         """
         Creates a :class:`PathlingContext` with the given configuration options. This should only
@@ -176,6 +179,9 @@ class PathlingContext:
                implementation and the code systems used.
         :param enable_delta: enables the use of Delta for storage of FHIR data.
                Only supported when no SparkSession is provided.
+        :param enable_remote_debugging: enables remote debugging for the JVM process.
+        :param debug_port: the port for the debugger to listen on (default: 5005)
+        :param debug_suspend: if true, the JVM will suspend until a debugger is attached
         :return: a :class:`PathlingContext` instance initialized with the specified configuration
         """
 
@@ -195,6 +201,13 @@ class PathlingContext:
                     "org.apache.spark.sql.delta.catalog.DeltaCatalog",
                 )
             )
+
+            # Add remote debugging configuration if enabled
+            if enable_remote_debugging:
+                suspend_option = "y" if debug_suspend else "n"
+                debug_options = f"-agentlib:jdwp=transport=dt_socket,server=y,suspend={suspend_option},address={debug_port}"
+                spark_builder = spark_builder.config("spark.driver.extraJavaOptions", debug_options)
+
             return spark_builder.getOrCreate()
 
         spark = spark or SparkSession.getActiveSession() or _new_spark_session()

{pathling-8.0.0.dev0 → pathling-8.0.0.dev1}/pathling/datasink.py

@@ -16,7 +16,9 @@
 from typing import Callable, Optional
 
 from pathling.core import SparkConversionsMixin, StringMapper
-from pathling.datasource import DataSource
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from pathling.datasource import DataSource
 
 
 class ImportMode:
@@ -49,7 +51,7 @@ class DataSinks(SparkConversionsMixin):
     A class for writing FHIR data to a variety of different targets.
     """
 
-    def __init__(self, datasource: DataSource):
+    def __init__(self, datasource: "DataSource"):
         SparkConversionsMixin.__init__(self, datasource.spark)
         self._datasinks = (
             self.spark._jvm.au.csiro.pathling.library.io.sink.DataSinkBuilder(