smart-fetch 0.1.0__tar.gz

smart_fetch-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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smart_fetch-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: smart-fetch
+Version: 0.1.0
+Summary: Fetch FHIR data from your EHR easily and completely
+Author-email: Michael Terry <michael.terry@childrens.harvard.edu>
+Requires-Python: >= 3.11
+Description-Content-Type: text/markdown
+License-Expression: Apache-2.0
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+License-File: LICENSE
+Requires-Dist: cumulus-fhir-support >= 1.5
+Requires-Dist: rich
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: ruff < 0.13 ; extra == "dev"
+Requires-Dist: ddt ; extra == "tests"
+Requires-Dist: httpx ; extra == "tests"
+Requires-Dist: pytest ; extra == "tests"
+Requires-Dist: pytest-cov ; extra == "tests"
+Requires-Dist: respx ; extra == "tests"
+Requires-Dist: time-machine ; extra == "tests"
+Project-URL: Homepage, https://github.com/smart-on-fhir/smart-fetch
+Provides-Extra: dev
+Provides-Extra: tests
+
+# SMART Fetch
+
+A tool for extracting FHIR data from your EHR.
+
+## Quick Start
+
+If you want to skip any description and dive right in:
+
+```shell
+pipx install smart-fetch
+
+smart-fetch export \
+  --fhir-url https://bulk-data.smarthealthit.org/fhir \
+  /tmp/export
+```
+
+After running the above, you'll have a bunch of NDJSON resource files sitting in `/tmp/export`.
+
+Run `smart-fetch --help` to learn more about the various options.
+
+## Initial Export
+
+SMART Fetch can do an initial pull from your EHR,
+with either a "bulk export" or by manually searching through resources 
+based on a list of patient MRNs,
+when bulk exporting is either not available or too slow.
+
+## Post-Processing Your Export
+
+Very often, the initial export from the EHR will be missing some useful data.
+There will be referenced Medications, Observations, and clinical notes that you need to manually
+download to have a complete set of data.
+
+SMART Fetch can help fill in those gaps by post-processing (or hydrating) your FHIR data.
+
+Mostly these hydration tasks focus on grabbing data now so that you'll always have it,
+no matter what happens with your EHR later.
+
+### Example Hydration Tasks
+
+- Inlining clinical notes from DiagnosticReport or DocumentReference
+  (it's more reliable to get the note once upfront, and then you have it forever)
+- Adding missing Observations (several EHRs don't provide
+  DiagnosticReport.result or Observation.hasMember linked
+  Observations by default in a search/export)
+- Downloading MedicationRequest.medicationReference linked
+  Medications (which can't normally be bulk exported but
+  are necessary for clinically interpreting a MedicationRequest)
+
+## Managing Exports Over Time
+
+Fetching data for a group is rarely as simple as a single export.
+You may want to export some resources separately, for performance reasons
+(e.g. Observations can take a long time).
+Or you may want to grab updates to the group's data over time.
+
+SMART Fetch can help with that, by keeping each export in its own subfolder
+for individual processing,
+but also pooling all the results together with symlinks for convenience.
+
+### Example
+
+```shell
+pipx install smart-fetch
+
+# Initial export
+smart-fetch export \
+  --fhir-url https://bulk-data.smarthealthit.org/fhir \
+  --type Encounter,Patient \
+  /tmp/export
+
+ls -l /tmp/export
+# 001.2025-06-26/
+# Encounter.001.ndjson.gz -> 001.2025-06-26/Encounter.001.ndjson.gz
+# Patient.001.ndjson.gz -> 001.2025-06-26/Patient.001.ndjson.gz
+
+# Second export with a --since date, a new resource, and a nickname for the export
+smart-fetch export \
+  --fhir-url https://bulk-data.smarthealthit.org/fhir \
+  --type Encounter,Patient,Condition \
+  --since 2020-01-01 \
+  --nickname second-run \
+  /tmp/export
+
+ls -l /tmp/export
+# 001.2025-06-26/
+# 002.second-run/
+# Condition.001.ndjson.gz -> 002.second-run/Condition.001.ndjson.gz
+# Encounter.001.ndjson.gz -> 001.2025-06-26/Encounter.001.ndjson.gz
+# Encounter.002.ndjson.gz -> 002.second-run/Encounter.001.ndjson.gz
+# Patient.001.ndjson.gz -> 001.2025-06-26/Patient.001.ndjson.gz
+# Patient.002.ndjson.gz -> 002.second-run/Patient.001.ndjson.gz
+```
+

smart_fetch-0.1.0/README.md

@@ -0,0 +1,93 @@
+# SMART Fetch
+
+A tool for extracting FHIR data from your EHR.
+
+## Quick Start
+
+If you want to skip any description and dive right in:
+
+```shell
+pipx install smart-fetch
+
+smart-fetch export \
+  --fhir-url https://bulk-data.smarthealthit.org/fhir \
+  /tmp/export
+```
+
+After running the above, you'll have a bunch of NDJSON resource files sitting in `/tmp/export`.
+
+Run `smart-fetch --help` to learn more about the various options.
+
+## Initial Export
+
+SMART Fetch can do an initial pull from your EHR,
+with either a "bulk export" or by manually searching through resources 
+based on a list of patient MRNs,
+when bulk exporting is either not available or too slow.
+
+## Post-Processing Your Export
+
+Very often, the initial export from the EHR will be missing some useful data.
+There will be referenced Medications, Observations, and clinical notes that you need to manually
+download to have a complete set of data.
+
+SMART Fetch can help fill in those gaps by post-processing (or hydrating) your FHIR data.
+
+Mostly these hydration tasks focus on grabbing data now so that you'll always have it,
+no matter what happens with your EHR later.
+
+### Example Hydration Tasks
+
+- Inlining clinical notes from DiagnosticReport or DocumentReference
+  (it's more reliable to get the note once upfront, and then you have it forever)
+- Adding missing Observations (several EHRs don't provide
+  DiagnosticReport.result or Observation.hasMember linked
+  Observations by default in a search/export)
+- Downloading MedicationRequest.medicationReference linked
+  Medications (which can't normally be bulk exported but
+  are necessary for clinically interpreting a MedicationRequest)
+
+## Managing Exports Over Time
+
+Fetching data for a group is rarely as simple as a single export.
+You may want to export some resources separately, for performance reasons
+(e.g. Observations can take a long time).
+Or you may want to grab updates to the group's data over time.
+
+SMART Fetch can help with that, by keeping each export in its own subfolder
+for individual processing,
+but also pooling all the results together with symlinks for convenience.
+
+### Example
+
+```shell
+pipx install smart-fetch
+
+# Initial export
+smart-fetch export \
+  --fhir-url https://bulk-data.smarthealthit.org/fhir \
+  --type Encounter,Patient \
+  /tmp/export
+
+ls -l /tmp/export
+# 001.2025-06-26/
+# Encounter.001.ndjson.gz -> 001.2025-06-26/Encounter.001.ndjson.gz
+# Patient.001.ndjson.gz -> 001.2025-06-26/Patient.001.ndjson.gz
+
+# Second export with a --since date, a new resource, and a nickname for the export
+smart-fetch export \
+  --fhir-url https://bulk-data.smarthealthit.org/fhir \
+  --type Encounter,Patient,Condition \
+  --since 2020-01-01 \
+  --nickname second-run \
+  /tmp/export
+
+ls -l /tmp/export
+# 001.2025-06-26/
+# 002.second-run/
+# Condition.001.ndjson.gz -> 002.second-run/Condition.001.ndjson.gz
+# Encounter.001.ndjson.gz -> 001.2025-06-26/Encounter.001.ndjson.gz
+# Encounter.002.ndjson.gz -> 002.second-run/Encounter.001.ndjson.gz
+# Patient.001.ndjson.gz -> 001.2025-06-26/Patient.001.ndjson.gz
+# Patient.002.ndjson.gz -> 002.second-run/Patient.001.ndjson.gz
+```

smart_fetch-0.1.0/pyproject.toml

@@ -0,0 +1,74 @@
+[project]
+name = "smart-fetch"
+requires-python = ">= 3.11"
+dependencies = [
+    "cumulus-fhir-support >= 1.5",
+    "rich",
+]
+authors = [
+  { name="Michael Terry", email="michael.terry@childrens.harvard.edu" },
+]
+readme = "README.md"
+license = "Apache-2.0"
+classifiers = [
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+dynamic = ["description", "version"]
+
+[project.optional-dependencies]
+tests = [
+    "ddt",
+    "httpx",
+    "pytest",
+    "pytest-cov",
+    "respx",
+    "time-machine",
+]
+dev = [
+    "pre-commit",
+    # Ruff is using minor versions for breaking changes until their 1.0 release.
+    # See https://docs.astral.sh/ruff/versioning/
+    "ruff < 0.13",  # keep in rough sync with pre-commit-config.yaml
+]
+
+[project.urls]
+"Homepage" = "https://github.com/smart-on-fhir/smart-fetch"
+
+[project.scripts]
+smart-fetch = "smart_fetch.cli.main:main_cli"
+
+[build-system]
+requires = ["flit_core >=3.12,<4"]
+build-backend = "flit_core.buildapi"
+
+[tool.flit.sdist]
+include = [
+    "docs/",
+    "tests/",
+    "LICENSE",
+]
+exclude = [
+    "**/.pytest_cache",
+]
+
+[tool.ruff]
+line-length = 100
+
+[tool.ruff.lint]
+allowed-confusables = ["’"]  # allow proper apostrophes
+select = [
+    "A",  # prevent using keywords that clobber python builtins
+    "E",  # pycodestyle
+    "F",  # pyflakes
+    "I",  # isort
+    "PLE",  # pylint errors
+    "RUF",  # the ruff developer's own rules
+    "S",  # bandit security warnings
+    "UP",  # alert you when better syntax is available in your python version
+]
+
+[tool.ruff.lint.per-file-ignores]
+"**/__init__.py" = ["F401"]  # init files hold API, so not using imports is intentional
+"tests/**" = ["S"]  # tests do suspicious stuff that's fine, actually

smart_fetch-0.1.0/smart_fetch/__init__.py

@@ -0,0 +1,3 @@
+"""Fetch FHIR data from your EHR easily and completely"""
+
+__version__ = "0.1.0"