Implement integration gateway base architecture

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
   test:
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
         poetry-version: [1.8.2]
     runs-on: ubuntu-latest
     steps:

README.md

@@ -155,7 +155,7 @@ Sandboxes provide a staging environment for testing and validating your pipeline
 import healthchain as hc
 
 from healthchain.pipeline import SummarizationPipeline
-from healthchain.use_cases import ClinicalDecisionSupport
+from healthchain.sandbox.use_cases import ClinicalDecisionSupport
 from healthchain.models import Card, Prefetch, CDSRequest
 from healthchain.data_generator import CdsDataGenerator
 from typing import List
@@ -192,7 +192,7 @@ The `ClinicalDocumentation` use case implements a real-time Clinical Documentati
 import healthchain as hc
 
 from healthchain.pipeline import MedicalCodingPipeline
-from healthchain.use_cases import ClinicalDocumentation
+from healthchain.sandbox.use_cases import ClinicalDocumentation
 from healthchain.models import CdaRequest, CdaResponse
 from fhir.resources.documentreference import DocumentReference
 
@@ -227,7 +227,7 @@ Ensure you run the following commands in your `mycds.py` file:
 
 ```python
 cds = MyCDS()
-cds.run_sandbox()
+cds.start_sandbox()
 ```
 This will populate your EHR client with the data generation method you have defined, send requests to your server for processing, and save the data in the `./output` directory.
 

configs/interop/cda/sections/allergies.yaml

@@ -69,7 +69,8 @@ template:
 
   # Clinical status observation configuration
   clinical_status_obs:
-    template_id: "2.16.840.1.113883.10.20.1.39"
+    template_id:
+      - "2.16.840.1.113883.10.20.1.39"
     code: "33999-4"
     code_system: "2.16.840.1.113883.6.1"
     code_system_name: "LOINC"

configs/templates/fhir_cda/note_entry.liquid

@@ -17,7 +17,7 @@
         "@value": "{{ resource.date | format_date: 'cda' }}"
       },
       {% endif %}
-      "text": "{{ resource.content[0].attachment.data | from_base64 }}"
+      "text": {{ resource.content[0].attachment.data | from_base64 | json }}
     }
   }
 }

configs/templates/fhir_cda/problem_entry.liquid

@@ -42,11 +42,13 @@
         },
         "statusCode": {"@code": "{{ config.template.problem_obs.status_code }}"},
         "effectiveTime": {
-          {% if resource.onsetDateTime %}
-          "low": {"@value": "{{ resource.onsetDateTime }}"}
-          {% endif %}
-          {% if resource.abatementDateTime %}
-          "high": {"@value": "{{ resource.abatementDateTime }}"}
+          {% if resource.onsetDateTime and resource.abatementDateTime %}
+            "low": {"@value": "{{ resource.onsetDateTime }}"},
+            "high": {"@value": "{{ resource.abatementDateTime }}"}
+          {% elsif resource.onsetDateTime %}
+            "low": {"@value": "{{ resource.onsetDateTime }}"}
+          {% elsif resource.abatementDateTime %}
+            "high": {"@value": "{{ resource.abatementDateTime }}"}
           {% endif %}
         },
         "value": {

cookbook/cds_discharge_summarizer_hf_chat.py

@@ -1,9 +1,9 @@
 import healthchain as hc
 
 from healthchain.pipeline import SummarizationPipeline
-from healthchain.use_cases import ClinicalDecisionSupport
 from healthchain.models import CDSRequest, CDSResponse, Prefetch
 from healthchain.data_generators import CdsDataGenerator
+from healthchain.sandbox.use_cases import ClinicalDecisionSupport
 
 from langchain_huggingface.llms import HuggingFaceEndpoint
 from langchain_huggingface import ChatHuggingFace

cookbook/cds_discharge_summarizer_hf_trf.py

@@ -1,7 +1,7 @@
 import healthchain as hc
 
 from healthchain.pipeline import SummarizationPipeline
-from healthchain.use_cases import ClinicalDecisionSupport
+from healthchain.sandbox.use_cases import ClinicalDecisionSupport
 from healthchain.models import Prefetch, CDSRequest, CDSResponse
 from healthchain.data_generators import CdsDataGenerator
 

docs/api/clients.md

@@ -1,3 +1,3 @@
 # Clients
 
-::: healthchain.clients.ehrclient
+::: healthchain.sandbox.clients.ehr.EHRClient

docs/api/use_cases.md

@@ -1,9 +1,9 @@
 # Use Cases
 
-::: healthchain.use_cases.cds
+::: healthchain.sandbox.use_cases.cds
 ::: healthchain.models.requests.cdsrequest
 ::: healthchain.models.responses.cdsresponse
 
-::: healthchain.use_cases.clindoc
+::: healthchain.sandbox.use_cases.clindoc
 ::: healthchain.models.requests.cdarequest
 ::: healthchain.models.responses.cdaresponse

docs/cookbook/cds_sandbox.md

@@ -86,7 +86,7 @@ We'll also need to implement the service method, which will process the request
 ```python
 import healthchain as hc
 
-from healthchain.use_cases import ClinicalDecisionSupport
+from healthchain.sandbox.use_cases import ClinicalDecisionSupport
 from healthchain.models import CDSRequest, CDSResponse
 
 @hc.sandbox
@@ -136,7 +136,7 @@ To finish our sandbox, we'll define a client function that loads the data genera
 ```python
 import healthchain as hc
 
-from healthchain.use_cases import ClinicalDecisionSupport
+from healthchain.sandbox.use_cases import ClinicalDecisionSupport
 from healthchain.models import CDSRequest, CDSResponse, Prefetch
 
 @hc.sandbox

docs/cookbook/notereader_sandbox.md

@@ -8,9 +8,10 @@ Full example coming soon!
 import healthchain as hc
 
 from healthchain.io import Document
-from healthchain.models.requests.cda import CdaRequest, CdaResponse
+from healthchain.models.requests import CdaRequest
+from healthchain.models.responses import CdaResponse
 from healthchain.pipeline.medicalcodingpipeline import MedicalCodingPipeline
-from healthchain.use_cases.clindoc import ClinicalDocumentation
+from healthchain.sandbox.use_cases import ClinicalDocumentation
 from healthchain.fhir import create_document_reference
 
 from spacy.tokens import Span

docs/quickstart.md

@@ -163,7 +163,7 @@ Every sandbox also requires a **client** function marked by `@hc.ehr` and a **se
 ```python
 import healthchain as hc
 
-from healthchain.use_cases import ClinicalDocumentation
+from healthchain.sandbox.use_cases import ClinicalDocumentation
 from healthchain.pipeline import MedicalCodingPipeline
 from healthchain.models import CdaRequest, CdaResponse
 from healthchain.fhir import create_document_reference
@@ -245,7 +245,7 @@ The `.generate_prefetch()` method is dependent on use case and workflow. For exa
     ```python
     import healthchain as hc
 
-    from healthchain.use_cases import ClinicalDecisionSupport
+    from healthchain.sandbox.use_cases import ClinicalDecisionSupport
     from healthchain.models import Prefetch
     from healthchain.data_generators import CdsDataGenerator
 
@@ -268,7 +268,7 @@ The `.generate_prefetch()` method is dependent on use case and workflow. For exa
 === "On its own"
     ```python
     from healthchain.data_generators import CdsDataGenerator
-    from healthchain.workflows import Workflow
+    from healthchain.sandbox.workflows import Workflow
 
     # Initialize data generator
     data_generator = CdsDataGenerator()

docs/reference/sandbox/client.md

@@ -12,7 +12,7 @@ You can optionally specify the number of requests to generate with the `num` par
     ```python
     import healthchain as hc
 
-    from healthchain.use_cases import ClinicalDocumentation
+    from healthchain.sandbox.use_cases import ClinicalDocumentation
     from healthchain.fhir import create_document_reference
 
     from fhir.resources.documentreference import DocumentReference
@@ -32,7 +32,7 @@ You can optionally specify the number of requests to generate with the `num` par
     ```python
     import healthchain as hc
 
-    from healthchain.use_cases import ClinicalDecisionSupport
+    from healthchain.sandbox.use_cases import ClinicalDecisionSupport
     from healthchain.models import Prefetch
 
     from fhir.resources.patient import Patient

docs/reference/sandbox/sandbox.md

@@ -33,7 +33,7 @@ Every sandbox also requires a [**Client**](./client.md) function marked by `@hc.
 import healthchain as hc
 
 from healthchain.pipeline import SummarizationPipeline
-from healthchain.use_cases import ClinicalDecisionSupport
+from healthchain.sandbox.use_cases import ClinicalDecisionSupport
 from healthchain.data_generators import CdsDataGenerator
 from healthchain.models import CDSRequest, Prefetch, CDSResponse
 

docs/reference/sandbox/service.md

@@ -14,7 +14,7 @@ Here are minimal examples for each use case:
     ```python
     import healthchain as hc
 
-    from healthchain.use_cases import ClinicalDocumentation
+    from healthchain.sandbox.use_cases import ClinicalDocumentation
     from healthchain.pipeline import MedicalCodingPipeline
     from healthchain.models import CdaRequest, CdaResponse
     from healthchain.fhir import create_document_reference
@@ -42,7 +42,7 @@ Here are minimal examples for each use case:
     ```python
     import healthchain as hc
 
-    from healthchain.use_cases import ClinicalDecisionSupport
+    from healthchain.sandbox.use_cases import ClinicalDecisionSupport
     from healthchain.pipeline import SummarizationPipeline
     from healthchain.models import CDSRequest, CDSResponse, Prefetch
     from fhir.resources.patient import Patient

docs/reference/utilities/data_generator.md

@@ -35,7 +35,7 @@ You can use the data generator within a client function or on its own.
 === "Within client"
     ```python
     import healthchain as hc
-    from healthchain.use_cases import ClinicalDecisionSupport
+    from healthchain.sandbox.use_cases import ClinicalDecisionSupport
     from healthchain.models import Prefetch
     from healthchain.data_generators import CdsDataGenerator
 
@@ -58,7 +58,7 @@ You can use the data generator within a client function or on its own.
 === "On its own"
     ```python
     from healthchain.data_generators import CdsDataGenerator
-    from healthchain.workflows import Workflow
+    from healthchain.sandbox.workflows import Workflow
 
     # Initialize data generator
     data_generator = CdsDataGenerator()

healthchain/__init__.py

@@ -1,13 +1,18 @@
 import logging
-from .utils.logger import add_handlers
+import warnings
 
-from .decorators import api, sandbox
-from .clients import ehr
+from .utils.logger import add_handlers
 from .config.base import ConfigManager, ValidationLevel
 
+from .sandbox.decorator import sandbox, api, ehr
+
+# Enable deprecation warnings
+warnings.filterwarnings("always", category=DeprecationWarning, module="healthchain")
+
 logger = logging.getLogger(__name__)
+
 add_handlers(logger)
 logger.setLevel(logging.INFO)
 
 # Export them at the top level
-__all__ = ["ehr", "api", "sandbox", "ConfigManager", "ValidationLevel"]
+__all__ = ["ConfigManager", "ValidationLevel", "api", "ehr", "sandbox"]

healthchain/data_generators/__init__.py

@@ -5,7 +5,7 @@
 from .proceduregenerators import ProcedureGenerator
 from .medicationadministrationgenerators import MedicationAdministrationGenerator
 from .medicationrequestgenerators import MedicationRequestGenerator
-from .cdsdatagenerator import CdsDataGenerator, Workflow
+from .cdsdatagenerator import CdsDataGenerator
 
 __all__ = [
     "EncounterGenerator",
@@ -16,5 +16,4 @@
     "MedicationAdministrationGenerator",
     "MedicationRequestGenerator",
     "CdsDataGenerator",
-    "Workflow",
 ]

healthchain/data_generators/cdsdatagenerator.py

@@ -5,11 +5,13 @@
 from typing import Callable, Dict, Optional, List
 from pathlib import Path
 
-from healthchain.base import Workflow
 from fhir.resources.resource import Resource
+
 from healthchain.data_generators.basegenerators import generator_registry
 from healthchain.models import Prefetch
 from healthchain.fhir import create_document_reference
+from healthchain.sandbox.workflows import Workflow
+
 
 logger = logging.getLogger(__name__)