Merge pull request #43 from FHIR-Aggregator/development

dev to main

Author: teslajoy

.dockerignore

@@ -0,0 +1,3 @@
+data/
+*.log
+*.json

Dockerfile

@@ -0,0 +1,24 @@
+FROM python:3.12
+
+WORKDIR /app
+
+COPY . /app/CDA2FHIR
+
+WORKDIR /app/CDA2FHIR
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    libpq-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip install --upgrade pip && \
+    pip install --no-cache-dir charset_normalizer idna certifi requests pydantic pytest click \
+    pathlib orjson tqdm uuid openpyxl pandas inflection iteration_utilities fhir.resources==7.1.0 \
+    sqlalchemy==2.0.31 gen3-tracker>=0.0.7rc1
+
+RUN pip install -e /app/CDA2FHIR
+
+RUN mkdir -p /app/CDA2FHIR/data/raw
+RUN mkdir -p /app/CDA2FHIR/data/META
+
+ENTRYPOINT ["/bin/bash"]

README.md

@@ -26,31 +26,50 @@ To run the transformer, ensure that [CDA](https://cda.readthedocs.io/en/latest/)
 Usage: cda2fhir transform [OPTIONS]
 
 Options:
-  -s, --save               Save FHIR ndjson to CDA2FHIR/data/META folder.
-                           [default: True]
+  -s, --save                 Save FHIR ndjson to CDA2FHIR/data/META folder.
+                             [default: True]
   -v, --verbose
-  -ns, --n_samples TEXT    Number of samples to randomly select - max 100.
-  -nd, --n_diagnosis TEXT  Number of diagnosis to randomly select - max 100.
-  -p, --path TEXT          Path to save the FHIR NDJSON files. default is
-                           CDA2FHIR/data/META.
-  --help                   Show this message and exit.
+  -ns, --n_samples TEXT      Number of samples to randomly select - max 100.
+  -nd, --n_diagnosis TEXT    Number of diagnosis to randomly select - max 100.
+  -nf, --n_files TEXT        Number of files to randomly select - max 100.
+  -f, --transform_files      Transform CDA files to FHIR DocumentReference and
+                             Group.
+  -t, --transform_treatment  Transform CDA treatment to all sub-hierarchy of
+                             FHIR MedicationAdministration ->
+                             SubstanceDefinitionRepresentation.
+  -c, --transform_condition  Transform CDA disease to Condition
+  -m, --transform_mutation   Transform CDA mutation to Observation
+  -p, --path TEXT            Path to save the FHIR NDJSON files. default is
+                             CDA2FHIR/data/META.
+  --help                     Show this message and exit.
 ``` 
 
 - example 
 ``` 
 cda2fhir transform 
 ``` 
 
-### Testing
-Current integration testing runs on all data and may take approximately _**2 hours**_.
+### FHIR data validation 
 
+#### Run validate
 ```
-pytest -cov 
+ cda2fhir validate --path data/META
+{'summary': {'Specimen': 742505, 'Medication': 214, 'Observation': 832864, 'ResearchStudy': 429, 'SubstanceDefinition': 214, 'BodyStructure': 135, 'Condition': 114804, 'ResearchSubject': 184888, 'MedicationAdministration': 38267, 'Patient': 159047, 'Substance': 214}}
 ```
-### FHIR data validation 
-For FHIR data validation please run: 
+
+This command will validate your FHIR entities and their reference relations to each other. It will also generate a summary count of all entities in each ndjson file. 
+
+NOTE: This process may take _**5 minutes**_ or more, depending on your platform or compute power due to the size of the current data.
+
+#### Check for a field ex. extension
+```bash
+awk '!/extension/ {exit 1}' data/META/ResearchSubject.ndjson && echo "Every line contains 'extension'" || echo "Not every line contains 'extension'"
 ```
-g3t meta validate <path to data/META folder with ndjson files> 
->>>> resources={'summary': {'Specimen': 715864, 'Observation': 724999, 'ResearchStudy': 423, 'BodyStructure': 180, 'Condition': 95288, 'ResearchSubject': 160662, 'Patient': 137522}}
+
+
+### Testing
+Current integration testing runs on all data and may take approximately _**2 hours**_.
+
 ```
-NOTE: This process may take more than _**5 minutes**_ due to the size of the current data.
+pytest -cov 
+```

cda2fhir/__init__.py

@@ -0,0 +1,5 @@
+from cda2fhir.patcher import apply_patches
+
+apply_patches()
+
+