pathling 8.0.0.dev5__tar.gz → 8.0.1.dev0__tar.gz

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Files changed (45) hide show
  1. pathling-8.0.1.dev0/LICENSE +227 -0
  2. {pathling-8.0.0.dev5/pathling.egg-info → pathling-8.0.1.dev0}/PKG-INFO +71 -32
  3. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/README.md +68 -17
  4. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/bulk.py +1 -1
  5. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/designation.py +2 -2
  6. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/display.py +2 -2
  7. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/encode_bundles.py +2 -2
  8. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/encode_resources.py +2 -2
  9. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/fhir_view.py +2 -2
  10. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/member_of.py +2 -2
  11. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/property_of.py +2 -2
  12. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/subsumes.py +2 -2
  13. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/translate.py +2 -2
  14. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/__init__.py +2 -2
  15. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/_version.py +2 -2
  16. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/bulk.py +1 -1
  17. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/coding.py +2 -2
  18. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/context.py +2 -2
  19. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/core.py +2 -2
  20. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/datasink.py +2 -2
  21. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/datasource.py +2 -2
  22. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/fhir.py +2 -2
  23. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/functions.py +2 -2
  24. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/spark.py +2 -2
  25. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/udfs.py +2 -2
  26. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0/pathling.egg-info}/PKG-INFO +71 -32
  27. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/setup.py +3 -3
  28. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_bulk.py +2 -2
  29. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_datasource.py +2 -2
  30. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_encoders.py +2 -2
  31. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_functions.py +2 -2
  32. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_spark.py +2 -2
  33. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_udfs.py +2 -2
  34. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_view.py +2 -2
  35. pathling-8.0.0.dev5/LICENSE +0 -176
  36. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/MANIFEST.in +0 -0
  37. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/data/bundles/Bennett146_Swaniawski813_704c9750-f6e6-473b-ee83-fbd48e07fe3f.json +0 -0
  38. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/data/bundles/Dino214_Parisian75_40d82b80-b682-cd8b-da6d-396809878641.json +0 -0
  39. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/data/resources/Condition.ndjson +0 -0
  40. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/data/resources/Patient.ndjson +0 -0
  41. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling.egg-info/SOURCES.txt +0 -0
  42. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling.egg-info/dependency_links.txt +0 -0
  43. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling.egg-info/requires.txt +0 -0
  44. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling.egg-info/top_level.txt +0 -0
  45. {pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/setup.cfg +0 -0
pathling-8.0.1.dev0/LICENSE ADDED
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{pathling-8.0.0.dev5/pathling.egg-info → pathling-8.0.1.dev0}/PKG-INFO RENAMED
@@ -1,10 +1,10 @@
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- Metadata-Version: 2.4
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+ Metadata-Version: 2.1
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  Name: pathling
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- Version: 8.0.0.dev5
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+ Version: 8.0.1.dev0
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  Summary: Python API for Pathling
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  Home-page: https://github.com/aehrc/pathling
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  Author: Australian e-Health Research Centre, CSIRO
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- Author-email: ontoserver-support@csiro.au
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+ Author-email: pathling@csiro.au
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  License: Apache License, version 2.0
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  Keywords: pathling,fhir,analytics,spark,standards,terminology
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  Classifier: Development Status :: 3 - Alpha
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  License-File: LICENSE
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  Requires-Dist: pyspark<3.6.0,>=3.5.2
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  Requires-Dist: deprecated>=1.2.13
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- Dynamic: author
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- Dynamic: author-email
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- Dynamic: classifier
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- Dynamic: description
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- Dynamic: description-content-type
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- Dynamic: home-page
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- Dynamic: keywords
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- Dynamic: license
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- Dynamic: license-file
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- Dynamic: requires-dist
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- Dynamic: requires-python
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- Dynamic: summary
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  Python API for Pathling
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  =======================
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- This is the Python API for [Pathling](https://pathling.csiro.au). It provides a
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- set of tools that aid the use of FHIR terminology services and FHIR data within
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+ This is the Python API for [Pathling](https://pathling.csiro.au). It provides a
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+ set of tools that aid the use of FHIR terminology services and FHIR data within
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  Python applications and data science workflows.
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  [View the API documentation &rarr;](https://pathling.csiro.au/docs/python/pathling.html)
@@ -103,6 +91,55 @@ patients = pc.encode_bundle(bundles, 'Patient')
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  patients.select('id', 'gender', 'birthDate').show()
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  ```
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+ ## Running SQL on FHIR views
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+
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+ The Pathling library leverages the SQL on FHIR specification to provide a way to
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+ project FHIR data into easy-to-use tabular forms.
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+
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+ Once you have transformed your FHIR data into tabular views, you can choose to
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+ keep it in a Spark dataframe and continue to work with in Apache Spark, or
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+ export it to Python or R dataframes or a variety of different file formats for
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+ use in the tool of your choice.
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+
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+ ```python
105
+ from pathling import PathlingContext
106
+
107
+ pc = PathlingContext.create()
108
+ data = pc.read.ndjson("/some/file/location")
109
+
110
+ result = data.view(
111
+ resource="Patient",
112
+ select=[
113
+ {"column": [{"path": "getResourceKey()", "name": "patient_id"}]},
114
+ {
115
+ "forEach": "address",
116
+ "column": [
117
+ {"path": "line.join('\\n')", "name": "street"},
118
+ {"path": "use", "name": "use"},
119
+ {"path": "city", "name": "city"},
120
+ {"path": "postalCode", "name": "zip"},
121
+ ],
122
+ },
123
+ ],
124
+ )
125
+
126
+ display(result)
127
+ ```
128
+
129
+ The result of this query would look something like this:
130
+
131
+ | patient_id | street | use | city | zip |
132
+ |------------|----------------------------|------|------------|-------|
133
+ | 1 | 398 Kautzer Walk Suite 62 | home | Barnstable | 02675 |
134
+ | 1 | 186 Nitzsche Forge | work | Revere | 02151 |
135
+ | 2 | 1087 Quitzon Club | home | Plymouth | NULL |
136
+ | 3 | 442 Bruen Arcade | home | Nantucket | NULL |
137
+ | 4 | 858 Miller Junction Apt 61 | work | Brockton | 02301 |
138
+
139
+ For a more comprehensive example demonstrating SQL on FHIR queries with multiple
140
+ views, complex transformations and joins, see
141
+ the [SQL on FHIR example](https://pathling.csiro.au/docs/libraries/examples/prostate-cancer.md).
142
+
106
143
  ## Terminology functions
107
144
 
108
145
  The library also provides a set of functions for querying a FHIR terminology
@@ -227,29 +264,31 @@ with_displays = exploded_parents.withColumn(
227
264
 
228
265
  Results in:
229
266
 
230
- | CODE | DESCRIPTION | PARENT | PARENT_DISPLAY |
231
- |-----------|---------------------------|-----------|--------------------------------------------|
232
- | 65363002 | Otitis media | 43275000 | Otitis |
233
- | 65363002 | Otitis media | 68996008 | Disorder of middle ear |
234
- | 16114001 | Fracture of ankle | 125603006 | Injury of ankle |
235
- | 16114001 | Fracture of ankle | 46866001 | Fracture of lower limb |
236
- | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
237
- | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
238
- | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
239
- | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
240
- | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
241
- | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
267
+ | CODE | DESCRIPTION | PARENT | PARENT_DISPLAY |
268
+ |-----------|-------------------|-----------|-----------------------------------------|
269
+ | 65363002 | Otitis media | 43275000 | Otitis |
270
+ | 65363002 | Otitis media | 68996008 | Disorder of middle ear |
271
+ | 16114001 | Fracture of ankle | 125603006 | Injury of ankle |
272
+ | 16114001 | Fracture of ankle | 46866001 | Fracture of lower limb |
273
+ | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
274
+ | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
275
+ | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
276
+ | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
277
+ | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
278
+ | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
242
279
 
243
280
  ### Retrieving designations
244
281
 
245
282
  Some terminologies contain additional display terms for codes. These can be used
246
- for language translations, synonyms, and more. You can query these terms using the `designation` function.
283
+ for language translations, synonyms, and more. You can query these terms using
284
+ the `designation` function.
247
285
 
248
286
  ```python
249
287
  # Get the synonyms for each code in the dataset.
250
288
  synonyms = csv.withColumn(
251
289
  "SYNONYMS",
252
- designation(to_snomed_coding(csv.CODE), Coding.of_snomed("900000000000013009")),
290
+ designation(to_snomed_coding(csv.CODE),
291
+ Coding.of_snomed("900000000000013009")),
253
292
  )
254
293
  # Split each synonyms into a separate row.
255
294
  exploded_synonyms = synonyms.selectExpr(
@@ -347,7 +386,7 @@ RUN pip install --quiet --no-cache-dir pathling && \
347
386
  fix-permissions "/home/${NB_USER}"
348
387
  ```
349
388
 
350
- Pathling is copyright © 2018-2023, Commonwealth Scientific and Industrial
389
+ Pathling is copyright © 2018-2025, Commonwealth Scientific and Industrial
351
390
  Research Organisation
352
391
  (CSIRO) ABN 41 687 119 230. Licensed under
353
392
  the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/README.md RENAMED
@@ -1,8 +1,8 @@
1
1
  Python API for Pathling
2
2
  =======================
3
3
 
4
- This is the Python API for [Pathling](https://pathling.csiro.au). It provides a
5
- set of tools that aid the use of FHIR terminology services and FHIR data within
4
+ This is the Python API for [Pathling](https://pathling.csiro.au). It provides a
5
+ set of tools that aid the use of FHIR terminology services and FHIR data within
6
6
  Python applications and data science workflows.
7
7
 
8
8
  [View the API documentation &rarr;](https://pathling.csiro.au/docs/python/pathling.html)
@@ -71,6 +71,55 @@ patients = pc.encode_bundle(bundles, 'Patient')
71
71
  patients.select('id', 'gender', 'birthDate').show()
72
72
  ```
73
73
 
74
+ ## Running SQL on FHIR views
75
+
76
+ The Pathling library leverages the SQL on FHIR specification to provide a way to
77
+ project FHIR data into easy-to-use tabular forms.
78
+
79
+ Once you have transformed your FHIR data into tabular views, you can choose to
80
+ keep it in a Spark dataframe and continue to work with in Apache Spark, or
81
+ export it to Python or R dataframes or a variety of different file formats for
82
+ use in the tool of your choice.
83
+
84
+ ```python
85
+ from pathling import PathlingContext
86
+
87
+ pc = PathlingContext.create()
88
+ data = pc.read.ndjson("/some/file/location")
89
+
90
+ result = data.view(
91
+ resource="Patient",
92
+ select=[
93
+ {"column": [{"path": "getResourceKey()", "name": "patient_id"}]},
94
+ {
95
+ "forEach": "address",
96
+ "column": [
97
+ {"path": "line.join('\\n')", "name": "street"},
98
+ {"path": "use", "name": "use"},
99
+ {"path": "city", "name": "city"},
100
+ {"path": "postalCode", "name": "zip"},
101
+ ],
102
+ },
103
+ ],
104
+ )
105
+
106
+ display(result)
107
+ ```
108
+
109
+ The result of this query would look something like this:
110
+
111
+ | patient_id | street | use | city | zip |
112
+ |------------|----------------------------|------|------------|-------|
113
+ | 1 | 398 Kautzer Walk Suite 62 | home | Barnstable | 02675 |
114
+ | 1 | 186 Nitzsche Forge | work | Revere | 02151 |
115
+ | 2 | 1087 Quitzon Club | home | Plymouth | NULL |
116
+ | 3 | 442 Bruen Arcade | home | Nantucket | NULL |
117
+ | 4 | 858 Miller Junction Apt 61 | work | Brockton | 02301 |
118
+
119
+ For a more comprehensive example demonstrating SQL on FHIR queries with multiple
120
+ views, complex transformations and joins, see
121
+ the [SQL on FHIR example](https://pathling.csiro.au/docs/libraries/examples/prostate-cancer.md).
122
+
74
123
  ## Terminology functions
75
124
 
76
125
  The library also provides a set of functions for querying a FHIR terminology
@@ -195,29 +244,31 @@ with_displays = exploded_parents.withColumn(
195
244
 
196
245
  Results in:
197
246
 
198
- | CODE | DESCRIPTION | PARENT | PARENT_DISPLAY |
199
- |-----------|---------------------------|-----------|--------------------------------------------|
200
- | 65363002 | Otitis media | 43275000 | Otitis |
201
- | 65363002 | Otitis media | 68996008 | Disorder of middle ear |
202
- | 16114001 | Fracture of ankle | 125603006 | Injury of ankle |
203
- | 16114001 | Fracture of ankle | 46866001 | Fracture of lower limb |
204
- | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
205
- | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
206
- | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
207
- | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
208
- | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
209
- | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
247
+ | CODE | DESCRIPTION | PARENT | PARENT_DISPLAY |
248
+ |-----------|-------------------|-----------|-----------------------------------------|
249
+ | 65363002 | Otitis media | 43275000 | Otitis |
250
+ | 65363002 | Otitis media | 68996008 | Disorder of middle ear |
251
+ | 16114001 | Fracture of ankle | 125603006 | Injury of ankle |
252
+ | 16114001 | Fracture of ankle | 46866001 | Fracture of lower limb |
253
+ | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
254
+ | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
255
+ | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
256
+ | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
257
+ | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
258
+ | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
210
259
 
211
260
  ### Retrieving designations
212
261
 
213
262
  Some terminologies contain additional display terms for codes. These can be used
214
- for language translations, synonyms, and more. You can query these terms using the `designation` function.
263
+ for language translations, synonyms, and more. You can query these terms using
264
+ the `designation` function.
215
265
 
216
266
  ```python
217
267
  # Get the synonyms for each code in the dataset.
218
268
  synonyms = csv.withColumn(
219
269
  "SYNONYMS",
220
- designation(to_snomed_coding(csv.CODE), Coding.of_snomed("900000000000013009")),
270
+ designation(to_snomed_coding(csv.CODE),
271
+ Coding.of_snomed("900000000000013009")),
221
272
  )
222
273
  # Split each synonyms into a separate row.
223
274
  exploded_synonyms = synonyms.selectExpr(
@@ -315,7 +366,7 @@ RUN pip install --quiet --no-cache-dir pathling && \
315
366
  fix-permissions "/home/${NB_USER}"
316
367
  ```
317
368
 
318
- Pathling is copyright © 2018-2023, Commonwealth Scientific and Industrial
369
+ Pathling is copyright © 2018-2025, Commonwealth Scientific and Industrial
319
370
  Research Organisation
320
371
  (CSIRO) ABN 41 687 119 230. Licensed under
321
372
  the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/bulk.py RENAMED
@@ -1,4 +1,4 @@
1
- # Copyright 2025 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
3
  #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/designation.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/display.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/encode_bundles.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/encode_resources.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/fhir_view.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/member_of.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/property_of.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/subsumes.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/examples/translate.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/__init__.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/_version.py RENAMED
@@ -2,8 +2,8 @@
2
2
  # Auto generated from POM project version.
3
3
  # Please do not modify.
4
4
  #
5
- __version__="8.0.0.dev5"
6
- __java_version__="8.0.0-SNAPSHOT"
5
+ __version__="8.0.1.dev0"
6
+ __java_version__="8.0.1-SNAPSHOT"
7
7
  __scala_version__="2.12"
8
8
  __delta_version__="3.3.2"
9
9
  __hadoop_version__="3.3.4"
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/bulk.py RENAMED
@@ -1,4 +1,4 @@
1
- # Copyright 2025 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
3
  #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/coding.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/context.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/core.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/datasink.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/datasource.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/fhir.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/functions.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/spark.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2025 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/pathling/udfs.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0/pathling.egg-info}/PKG-INFO RENAMED
@@ -1,10 +1,10 @@
1
- Metadata-Version: 2.4
1
+ Metadata-Version: 2.1
2
2
  Name: pathling
3
- Version: 8.0.0.dev5
3
+ Version: 8.0.1.dev0
4
4
  Summary: Python API for Pathling
5
5
  Home-page: https://github.com/aehrc/pathling
6
6
  Author: Australian e-Health Research Centre, CSIRO
7
- Author-email: ontoserver-support@csiro.au
7
+ Author-email: pathling@csiro.au
8
8
  License: Apache License, version 2.0
9
9
  Keywords: pathling,fhir,analytics,spark,standards,terminology
10
10
  Classifier: Development Status :: 3 - Alpha
@@ -17,24 +17,12 @@ Description-Content-Type: text/markdown
17
17
  License-File: LICENSE
18
18
  Requires-Dist: pyspark<3.6.0,>=3.5.2
19
19
  Requires-Dist: deprecated>=1.2.13
20
- Dynamic: author
21
- Dynamic: author-email
22
- Dynamic: classifier
23
- Dynamic: description
24
- Dynamic: description-content-type
25
- Dynamic: home-page
26
- Dynamic: keywords
27
- Dynamic: license
28
- Dynamic: license-file
29
- Dynamic: requires-dist
30
- Dynamic: requires-python
31
- Dynamic: summary
32
20
 
33
21
  Python API for Pathling
34
22
  =======================
35
23
 
36
- This is the Python API for [Pathling](https://pathling.csiro.au). It provides a
37
- set of tools that aid the use of FHIR terminology services and FHIR data within
24
+ This is the Python API for [Pathling](https://pathling.csiro.au). It provides a
25
+ set of tools that aid the use of FHIR terminology services and FHIR data within
38
26
  Python applications and data science workflows.
39
27
 
40
28
  [View the API documentation &rarr;](https://pathling.csiro.au/docs/python/pathling.html)
@@ -103,6 +91,55 @@ patients = pc.encode_bundle(bundles, 'Patient')
103
91
  patients.select('id', 'gender', 'birthDate').show()
104
92
  ```
105
93
 
94
+ ## Running SQL on FHIR views
95
+
96
+ The Pathling library leverages the SQL on FHIR specification to provide a way to
97
+ project FHIR data into easy-to-use tabular forms.
98
+
99
+ Once you have transformed your FHIR data into tabular views, you can choose to
100
+ keep it in a Spark dataframe and continue to work with in Apache Spark, or
101
+ export it to Python or R dataframes or a variety of different file formats for
102
+ use in the tool of your choice.
103
+
104
+ ```python
105
+ from pathling import PathlingContext
106
+
107
+ pc = PathlingContext.create()
108
+ data = pc.read.ndjson("/some/file/location")
109
+
110
+ result = data.view(
111
+ resource="Patient",
112
+ select=[
113
+ {"column": [{"path": "getResourceKey()", "name": "patient_id"}]},
114
+ {
115
+ "forEach": "address",
116
+ "column": [
117
+ {"path": "line.join('\\n')", "name": "street"},
118
+ {"path": "use", "name": "use"},
119
+ {"path": "city", "name": "city"},
120
+ {"path": "postalCode", "name": "zip"},
121
+ ],
122
+ },
123
+ ],
124
+ )
125
+
126
+ display(result)
127
+ ```
128
+
129
+ The result of this query would look something like this:
130
+
131
+ | patient_id | street | use | city | zip |
132
+ |------------|----------------------------|------|------------|-------|
133
+ | 1 | 398 Kautzer Walk Suite 62 | home | Barnstable | 02675 |
134
+ | 1 | 186 Nitzsche Forge | work | Revere | 02151 |
135
+ | 2 | 1087 Quitzon Club | home | Plymouth | NULL |
136
+ | 3 | 442 Bruen Arcade | home | Nantucket | NULL |
137
+ | 4 | 858 Miller Junction Apt 61 | work | Brockton | 02301 |
138
+
139
+ For a more comprehensive example demonstrating SQL on FHIR queries with multiple
140
+ views, complex transformations and joins, see
141
+ the [SQL on FHIR example](https://pathling.csiro.au/docs/libraries/examples/prostate-cancer.md).
142
+
106
143
  ## Terminology functions
107
144
 
108
145
  The library also provides a set of functions for querying a FHIR terminology
@@ -227,29 +264,31 @@ with_displays = exploded_parents.withColumn(
227
264
 
228
265
  Results in:
229
266
 
230
- | CODE | DESCRIPTION | PARENT | PARENT_DISPLAY |
231
- |-----------|---------------------------|-----------|--------------------------------------------|
232
- | 65363002 | Otitis media | 43275000 | Otitis |
233
- | 65363002 | Otitis media | 68996008 | Disorder of middle ear |
234
- | 16114001 | Fracture of ankle | 125603006 | Injury of ankle |
235
- | 16114001 | Fracture of ankle | 46866001 | Fracture of lower limb |
236
- | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
237
- | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
238
- | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
239
- | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
240
- | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
241
- | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
267
+ | CODE | DESCRIPTION | PARENT | PARENT_DISPLAY |
268
+ |-----------|-------------------|-----------|-----------------------------------------|
269
+ | 65363002 | Otitis media | 43275000 | Otitis |
270
+ | 65363002 | Otitis media | 68996008 | Disorder of middle ear |
271
+ | 16114001 | Fracture of ankle | 125603006 | Injury of ankle |
272
+ | 16114001 | Fracture of ankle | 46866001 | Fracture of lower limb |
273
+ | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
274
+ | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
275
+ | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
276
+ | 444814009 | Viral sinusitis | 36971009 | Sinusitis |
277
+ | 444814009 | Viral sinusitis | 281794004 | Viral upper respiratory tract infection |
278
+ | 444814009 | Viral sinusitis | 363166002 | Infective disorder of head |
242
279
 
243
280
  ### Retrieving designations
244
281
 
245
282
  Some terminologies contain additional display terms for codes. These can be used
246
- for language translations, synonyms, and more. You can query these terms using the `designation` function.
283
+ for language translations, synonyms, and more. You can query these terms using
284
+ the `designation` function.
247
285
 
248
286
  ```python
249
287
  # Get the synonyms for each code in the dataset.
250
288
  synonyms = csv.withColumn(
251
289
  "SYNONYMS",
252
- designation(to_snomed_coding(csv.CODE), Coding.of_snomed("900000000000013009")),
290
+ designation(to_snomed_coding(csv.CODE),
291
+ Coding.of_snomed("900000000000013009")),
253
292
  )
254
293
  # Split each synonyms into a separate row.
255
294
  exploded_synonyms = synonyms.selectExpr(
@@ -347,7 +386,7 @@ RUN pip install --quiet --no-cache-dir pathling && \
347
386
  fix-permissions "/home/${NB_USER}"
348
387
  ```
349
388
 
350
- Pathling is copyright © 2018-2023, Commonwealth Scientific and Industrial
389
+ Pathling is copyright © 2018-2025, Commonwealth Scientific and Industrial
351
390
  Research Organisation
352
391
  (CSIRO) ABN 41 687 119 230. Licensed under
353
392
  the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/setup.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
@@ -50,7 +50,7 @@ setup(
50
50
  long_description=long_description,
51
51
  long_description_content_type="text/markdown",
52
52
  author="Australian e-Health Research Centre, CSIRO",
53
- author_email="ontoserver-support@csiro.au",
53
+ author_email="pathling@csiro.au",
54
54
  url="https://github.com/aehrc/pathling",
55
55
  keywords=["pathling", "fhir", "analytics", "spark", "standards", "terminology"],
56
56
  classifiers=[
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_bulk.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_datasource.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_encoders.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_functions.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_spark.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_udfs.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/tests/test_view.py RENAMED
@@ -1,6 +1,6 @@
1
- # Copyright 2023 Commonwealth Scientific and Industrial Research
1
+ # Copyright © 2018-2025 Commonwealth Scientific and Industrial Research
2
2
  # Organisation (CSIRO) ABN 41 687 119 230.
3
- #
3
+ #
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
5
5
  # you may not use this file except in compliance with the License.
6
6
  # You may obtain a copy of the License at
pathling-8.0.0.dev5/LICENSE DELETED
@@ -1,176 +0,0 @@
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{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/MANIFEST.in RENAMED
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{pathling-8.0.0.dev5 → pathling-8.0.1.dev0}/setup.cfg RENAMED
File without changes