pathling 9.6.0.dev0__tar.gz → 9.7.0__tar.gz

{pathling-9.6.0.dev0 → pathling-9.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pathling
-Version: 9.6.0.dev0
+Version: 9.7.0
 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-9.6.0.dev0 → pathling-9.7.0}/examples/bulk.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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

pathling-9.7.0/examples/designation.py

@@ -0,0 +1,40 @@
+#
+# Copyright © 2018-2026 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 Coding, PathlingContext, designation, to_snomed_coding
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+pc = PathlingContext.create()
+
+csv = pc.spark.read.options(header=True).csv(
+    f"file://{os.path.join(HERE, 'data/csv/conditions.csv')}"
+)
+
+# Obtain display name for snomed codes
+
+SNOMED_FULLY_SPECIFIED_NAME = Coding.of_snomed("900000000000003001")
+
+result = csv.withColumn(
+    "FULL_NAME",
+    designation(to_snomed_coding(csv.CODE), SNOMED_FULLY_SPECIFIED_NAME, "en").getItem(
+        0
+    ),
+)
+result.select("CODE", "DESCRIPTION", "FULL_NAME").show()

pathling-9.7.0/examples/display.py

@@ -0,0 +1,32 @@
+#
+# Copyright © 2018-2026 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, display, to_snomed_coding
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+pc = PathlingContext.create()
+
+csv = pc.spark.read.options(header=True).csv(
+    f"file://{os.path.join(HERE, 'data/csv/conditions.csv')}"
+)
+
+# Obtain display name for snomed codes
+result = csv.withColumn("DISPLAY_NAME", display(to_snomed_coding(csv.CODE)))
+result.select("CODE", "DESCRIPTION", "DISPLAY_NAME").show()

pathling-9.7.0/examples/encode_bundles.py

@@ -0,0 +1,37 @@
+#
+# Copyright © 2018-2026 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__))
+
+pc = PathlingContext.create()
+
+# Read each Bundle into a row within a Spark data set.
+bundles_dir = os.path.join(HERE, "data/bundles/")
+bundles = pc.spark.read.text(bundles_dir, wholetext=True)
+
+# Convert the data set of strings into a structured FHIR data set.
+patients = pc.encode_bundle(bundles, "Patient")
+
+# JSON is the default format, XML Bundles can be encoded using input type.
+# patients = pc.encodeBundle(bundles, 'Patient', inputType=MimeType.FHIR_XML)
+
+# Do some stuff.
+patients.select("id", "gender", "birthDate").show()

pathling-9.7.0/examples/encode_resources.py

@@ -0,0 +1,34 @@
+#
+# Copyright © 2018-2026 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__))
+
+pc = PathlingContext.create()
+
+# Read each line from the NDJSON into a row within a Spark data set.
+ndjson_dir = os.path.join(HERE, "data/resources/")
+json_resources = pc.spark.read.text(ndjson_dir)
+
+# Convert the data set of strings into a structured FHIR data set.
+patients = pc.encode(json_resources, "Patient")
+
+# Do some stuff.
+patients.select("id", "gender", "birthDate").show()

pathling-9.7.0/examples/fhir_search.py

@@ -0,0 +1,32 @@
+#
+# Copyright © 2018-2026 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-9.6.0.dev0 → pathling-9.7.0}/examples/fhir_view.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/examples/member_of.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/examples/property_of.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/examples/subsumes.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/examples/translate.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/__init__.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 .coding import Coding
 from .context import PathlingContext, StorageType

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/_version.py

@@ -2,8 +2,8 @@
 # Auto generated from POM project version.
 # Please do not modify.
 #
-__version__="9.6.0.dev0"
-__java_version__="9.6.0-SNAPSHOT"
+__version__="9.7.0"
+__java_version__="9.7.0-SNAPSHOT"
 __scala_version__="2.13"
 __delta_version__="4.0.0"
 __hadoop_version__="3.4.1"

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/bulk.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 dataclasses import dataclass
 from datetime import datetime, timezone

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/coding.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 typing import Optional
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/context.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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.
 
 # noinspection PyPackageRequirements
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/core.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 typing import Any, Callable, Optional, Sequence, Tuple, Union
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/datasink.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 dataclasses import dataclass
 from typing import TYPE_CHECKING, Callable, List, Optional

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/datasource.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 json import dumps, loads

pathling-9.7.0/pathling/fhir.py

@@ -0,0 +1,33 @@
+#
+# Copyright © 2018-2026 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.
+#
+
+
+class MimeType:
+    """
+    Constants for FHIR encoding mime types.
+    """
+
+    FHIR_JSON: str = "application/fhir+json"
+    FHIR_XML: str = "application/fhir+xml"
+
+
+class Version:
+    """
+    Constants for FHIR versions.
+    """
+
+    R4: str = "R4"

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/functions.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 urllib.parse
 from typing import Optional

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/spark.py

@@ -1,18 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 uuid
 

{pathling-9.6.0.dev0 → pathling-9.7.0}/pathling/udfs.py

@@ -1,17 +1,19 @@
-#  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
+# Copyright © 2018-2026 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+# 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.
 #
-#  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 typing import Any, Collection, Optional, Union
 

pathling-9.6.0.dev0/examples/designation.py

@@ -1,38 +0,0 @@
-#  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 Coding, PathlingContext, designation, to_snomed_coding
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-
-pc = PathlingContext.create()
-
-csv = pc.spark.read.options(header=True).csv(
-    f"file://{os.path.join(HERE, 'data/csv/conditions.csv')}"
-)
-
-# Obtain display name for snomed codes
-
-SNOMED_FULLY_SPECIFIED_NAME = Coding.of_snomed("900000000000003001")
-
-result = csv.withColumn(
-    "FULL_NAME",
-    designation(to_snomed_coding(csv.CODE), SNOMED_FULLY_SPECIFIED_NAME, "en").getItem(
-        0
-    ),
-)
-result.select("CODE", "DESCRIPTION", "FULL_NAME").show()

pathling-9.6.0.dev0/examples/display.py

@@ -1,30 +0,0 @@
-#  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, display, to_snomed_coding
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-
-pc = PathlingContext.create()
-
-csv = pc.spark.read.options(header=True).csv(
-    f"file://{os.path.join(HERE, 'data/csv/conditions.csv')}"
-)
-
-# Obtain display name for snomed codes
-result = csv.withColumn("DISPLAY_NAME", display(to_snomed_coding(csv.CODE)))
-result.select("CODE", "DESCRIPTION", "DISPLAY_NAME").show()

pathling-9.6.0.dev0/examples/encode_bundles.py

@@ -1,35 +0,0 @@
-#  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__))
-
-pc = PathlingContext.create()
-
-# Read each Bundle into a row within a Spark data set.
-bundles_dir = os.path.join(HERE, "data/bundles/")
-bundles = pc.spark.read.text(bundles_dir, wholetext=True)
-
-# Convert the data set of strings into a structured FHIR data set.
-patients = pc.encode_bundle(bundles, "Patient")
-
-# JSON is the default format, XML Bundles can be encoded using input type.
-# patients = pc.encodeBundle(bundles, 'Patient', inputType=MimeType.FHIR_XML)
-
-# Do some stuff.
-patients.select("id", "gender", "birthDate").show()

pathling-9.6.0.dev0/examples/encode_resources.py

@@ -1,32 +0,0 @@
-#  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__))
-
-pc = PathlingContext.create()
-
-# Read each line from the NDJSON into a row within a Spark data set.
-ndjson_dir = os.path.join(HERE, "data/resources/")
-json_resources = pc.spark.read.text(ndjson_dir)
-
-# Convert the data set of strings into a structured FHIR data set.
-patients = pc.encode(json_resources, "Patient")
-
-# Do some stuff.
-patients.select("id", "gender", "birthDate").show()

pathling-9.6.0.dev0/examples/fhir_search.py

@@ -1,30 +0,0 @@
-#  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-9.6.0.dev0/pathling/fhir.py

@@ -1,31 +0,0 @@
-#  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.
-
-
-class MimeType:
-    """
-    Constants for FHIR encoding mime types.
-    """
-
-    FHIR_JSON: str = "application/fhir+json"
-    FHIR_XML: str = "application/fhir+xml"
-
-
-class Version:
-    """
-    Constants for FHIR versions.
-    """
-
-    R4: str = "R4"