Add fhirpathpy as dependency (#62)

* Add fhirpathpy as dependency * Fix workflow to not install fhirpathpy
UMEssen · Jul 1, 2022 · 1f156b2 · 1f156b2
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Showing 5 changed files with 9 additions and 53 deletions.
diff --git a/.github/workflows/mypy-flake-test.yml b/.github/workflows/mypy-flake-test.yml
@@ -45,7 +45,6 @@ jobs:
           export PATH="/root/.local/bin:$PATH"
           poetry run pip install -U pip
           poetry install -E all
-          pip install git+https://github.com/beda-software/fhirpath-py.git
       - name: Run MyPy
         run: |
           poetry run mypy --install-types --non-interactive fhir_pyrate/

diff --git a/README.md b/README.md
@@ -82,12 +82,6 @@ pip install "fhir-pyrate[downloader]" # only for downloader
 pip install "fhir-pyrate[all]" # for both
 ```
 
-If you want to use the FHIRPath capabilities you also need to
-install [fhirpath-py](https://github.com/beda-software/fhirpath-py) with
-```bash
-pip install git+https://github.com/beda-software/fhirpath-py.git
-```
-
 ### Or Within Poetry
 We can also use poetry for this same purpose. Using PyPi we need to run the following commands.
 ```bash
@@ -122,11 +116,6 @@ or by adding the following to your `pyproject.toml` file:
 fhir-pyrate = {git = "https://github.com/UMEssen/FHIR-PYrate.git", branch = "main", extras = ["all"]}
 ```
 
-And if you want to use FHIRPaths, add [fhirpath-py](https://github.com/beda-software/fhirpath-py).
-```bash
-poetry add git+https://github.com/beda-software/fhirpath-py.git
-```
-
 ## Run Tests
 
 When implementing new features, make sure that the existing ones have not been broken by using our
@@ -364,13 +353,6 @@ df = search.bundles_to_dataframe(
     fhir_paths=["id", ("code", "code.coding"), ("identifier", "identifier[0].code")],
 )
 ```
-**NOTE on [fhirpath-py](https://github.com/beda-software/fhirpath-py)**: This package is
-currently not on PyPi and
-[PyPi does not allow packages that are not on PyPi](https://github.com/pypa/pip/issues/6301),
-so if you want to use this feature you need to install the package separately or use:
-```
-pip install git+https://github.com/UMEssen/FHIR-PYrate.git
-```
 **NOTE 1 on FHIR paths**: The standard also allows some primitive math operations such as modulus
 (`mod`) or integer division (`div`), and this may be problematic if there are fields of the
 resource that use these terms as attributes.

diff --git a/fhir_pyrate/pirate.py b/fhir_pyrate/pirate.py
@@ -14,6 +14,7 @@
 import pandas as pd
 import requests
 from dateutil.parser import parse
+from fhirpathpy import compile
 from tqdm import tqdm
 
 from fhir_pyrate import Ahoy
@@ -52,13 +53,6 @@ class Pirate:
         "xor",
         "implies",
     ]
-    FHIRPATH_IMPORT_ERROR = (
-        "The fhirpath-py package cannot be pushed as a package dependency because it is not "
-        "present on PyPi, if you want to use the FHIRPath functionalities you need to install "
-        "this package using "
-        "`pip install git+https://github.com/beda-software/fhirpath-py.git` or by adding it to "
-        "poetry."
-    )
 
     def __init__(
         self,
@@ -641,10 +635,6 @@ class whenever the creation of a DataFrame happens directly after the query
         ```
         """
         if fhir_paths is not None:
-            try:
-                from fhirpathpy import compile
-            except ImportError as e:
-                raise ImportError(self.FHIRPATH_IMPORT_ERROR) from e
             logger.debug(
                 f"The selected process_function {process_function.__name__} will be "
                 f"overwritten."
@@ -748,11 +738,6 @@ def trade_rows_for_dataframe(
         :return: A pandas DataFrame containing the queried information merged with the original
         DataFrame
         """
-        if fhir_paths is not None:
-            try:
-                import fhirpathpy  # noqa
-            except ImportError as e:
-                raise ImportError(self.FHIRPATH_IMPORT_ERROR) from e
         request_params = {} if request_params is None else request_params
         logger.info(
             f"Querying each row of the DataFrame with {self.num_processes} processes."
@@ -850,11 +835,6 @@ class whenever the creation of a DataFrame happens directly after the query
         please refer to the documentation of the respective methods.
         :return: A pandas DataFrame containing the queried information
         """
-        if fhir_paths is not None:
-            try:
-                import fhirpathpy  # noqa
-            except ImportError as e:
-                raise ImportError(self.FHIRPATH_IMPORT_ERROR) from e
         return self.bundles_to_dataframe(
             bundles=bundles_function(**kwargs),
             process_function=process_function,

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,6 +27,7 @@ pandas = "^1.3.0"
 tqdm = "^4.56.0"
 requests = "^2.28.0"
 PyJWT = "^2.4.0"
+fhirpathpy = "^0.1.0"
 
 
 [tool.poetry.extras]
@@ -36,7 +37,6 @@ all = ["SimpleITK", "pydicom", "dicomweb-client", "spacy"]
 
 [tool.poetry.dev-dependencies]
 python-dotenv = "^0.20.0"
-fhirpathpy = {git = "https://github.com/beda-software/fhirpath-py.git"}
 pre-commit = "^2.14.0"
 flake8 = "3.9.2"
 mypy = "0.910"