Update tests and docs

README.md

@@ -96,7 +96,11 @@ Pre-built pipelines are use case specific end-to-end workflows that already have
 from healthchain.pipeline import MedicalCodingPipeline
 from healthchain.models import CdaRequest
 
-pipeline = MedicalCodingPipeline.load("./path/to/model")
+# Load from model ID
+pipeline = MedicalCodingPipeline.from_model_id("en_core_sci_md", source="spacy")
+
+# Or load from local model
+pipeline = MedicalCodingPipeline.from_local_model("./path/to/model", source="spacy")
 
 cda_data = CdaRequest(document="<CDA XML content>")
 output = pipeline(cda_data)
@@ -129,7 +133,9 @@ from typing import List
 @hc.sandbox
 class MyCDS(ClinicalDecisionSupport):
     def __init__(self) -> None:
-        self.pipeline = SummarizationPipeline.load("./path/to/model")
+        self.pipeline = SummarizationPipeline.from_model_id(
+            "DISLab/SummLlama3.2-3B", source="huggingface"
+        )
         self.data_generator = CdsDataGenerator()
 
     # Sets up an instance of a mock EHR client of the specified workflow
@@ -162,7 +168,9 @@ from healthchain.models import CcdData, CdaRequest, CdaResponse
 @hc.sandbox
 class NotereaderSandbox(ClinicalDocumentation):
     def __init__(self):
-        self.pipeline = MedicalCodingPipeline.load("./path/to/model")
+        self.pipeline = MedicalCodingPipeline.from_model_id(
+            "en_core_sci_md", source="spacy"
+        )
 
     # Load an existing CDA file
     @hc.ehr(workflow="sign-note-inpatient")

docs/cookbook/notereader_sandbox.md

@@ -18,7 +18,9 @@ from healthchain.models import (
 class NotereaderSandbox(ClinicalDocumentation):
   def __init__(self):
       self.cda_path = "./resources/uclh_cda.xml"
-      self.pipeline = MedicalCodingPipeline.load("./resources/models/medcat_model.zip")
+      self.pipeline = MedicalCodingPipeline.from_local_model(
+          "./resources/models/medcat_model.zip", source="spacy"
+      )
 
   @hc.ehr(workflow="sign-note-inpatient")
   def load_data_in_client(self) -> CcdData:

docs/quickstart.md

@@ -100,7 +100,15 @@ For a full list of available prebuilt pipelines and details on how to configure
 from healthchain.pipeline import MedicalCodingPipeline
 from healthchain.models import CdaRequest
 
-pipeline = MedicalCodingPipeline.load("./path/to/model")
+# Load from pre-built chain
+chain = ChatPromptTemplate.from_template("Summarize: {text}") | ChatOpenAI()
+pipeline = MedicalCodingPipeline.load(chain, source="langchain")
+
+# Or load from model ID
+pipeline = MedicalCodingPipeline.from_model_id("DISLab/SummLlama3-8B", source="huggingface")
+
+# Or load from local model
+pipeline = MedicalCodingPipeline.from_local_model("./path/to/model", source="spacy")
 
 cda_data = CdaRequest(document="<CDA XML content>")
 output = pipeline(cda_data)
@@ -128,7 +136,9 @@ from healthchain.models import CdaRequest, CdaResponse, CcdData
 class MyCoolSandbox(ClinicalDocumentation):
     def __init__(self) -> None:
         # Load your pipeline
-        self.pipeline = MedicalCodingPipeline.load("./path/to/model")
+        self.pipeline = MedicalCodingPipeline.from_local_model(
+            "./path/to/model", source="spacy"
+        )
 
     @hc.ehr(workflow="sign-note-inpatient")
     def load_data_in_client(self) -> CcdData:

tests/components/conftest.py

@@ -1,5 +1,6 @@
 import pytest
 from healthchain.io.containers.document import Document
+from healthchain.pipeline.components import CdsCardCreator
 from tests.pipeline.conftest import mock_spacy_nlp  # noqa: F401
 
 
@@ -14,3 +15,21 @@ def sample_lookup():
 @pytest.fixture
 def sample_document():
     return Document(data="This is a sample text for testing.")
+
+
+@pytest.fixture
+def basic_creator():
+    return CdsCardCreator()
+
+
+@pytest.fixture
+def custom_template_creator():
+    template = """
+    {
+        "summary": "Custom: {{ model_output }}",
+        "indicator": "warning",
+        "source": {{ default_source | tojson }},
+        "detail": "{{ model_output }}"
+    }
+    """
+    return CdsCardCreator(template=template)

tests/components/test_cardcreator.py

@@ -4,24 +4,6 @@
 from healthchain.models.responses.cdsresponse import Card, Source, IndicatorEnum
 
 
-@pytest.fixture
-def basic_creator():
-    return CdsCardCreator()
-
-
-@pytest.fixture
-def custom_template_creator():
-    template = """
-    {
-        "summary": "Custom: {{ model_output }}",
-        "indicator": "warning",
-        "source": {{ default_source | tojson }},
-        "detail": "{{ model_output }}"
-    }
-    """
-    return CdsCardCreator(template=template)
-
-
 def test_default_template_rendering(basic_creator):
     content = "Test message"
     card = basic_creator.create_card(content)
@@ -109,3 +91,50 @@ def test_invalid_input_configuration():
         "Either model output (source and task) or content need to be provided"
         in str(exc_info.value)
     )
+
+
+def test_template_file_loading(tmp_path):
+    # Create a temporary template file
+    template_file = tmp_path / "test_template.json"
+    template_content = """
+    {
+        "summary": "File Template: {{ model_output }}",
+        "indicator": "warning",
+        "source": {{ default_source | tojson }},
+        "detail": "{{ model_output }}"
+    }
+    """
+    template_file.write_text(template_content)
+
+    creator = CdsCardCreator(template_path=template_file)
+    card = creator.create_card("Test message")
+
+    assert card.summary == "File Template: Test message"
+    assert card.indicator == IndicatorEnum.warning
+    assert card.source == Source(label="Card Generated by HealthChain")
+    assert card.detail == "Test message"
+
+
+def test_nonexistent_template_file(caplog):
+    creator = CdsCardCreator(template_path="nonexistent_template.json")
+    card = creator.create_card("Test message")
+    assert card.summary == "Test message"
+    assert card.indicator == IndicatorEnum.info
+    assert card.source == Source(label="Card Generated by HealthChain")
+    assert card.detail == "Test message"
+    assert "Error loading template" in caplog.text
+
+
+def test_invalid_template_file(tmp_path):
+    # Create a temporary template file with invalid JSON
+    template_file = tmp_path / "invalid_template.json"
+    template_content = """
+    {
+        "summary": {{ invalid_json }},
+        "indicator": "warning"
+    """  # Invalid JSON
+    template_file.write_text(template_content)
+
+    with pytest.raises(ValueError):
+        creator = CdsCardCreator(template_path=template_file)
+        creator.create_card("Test message")

tests/pipeline/prebuilt/test_medicalcoding.py

@@ -37,8 +37,9 @@ def test_coding_pipeline(mock_cda_connector, mock_spacy_nlp):
             ModelConfig(
                 source=ModelSource.SPACY,
                 model="en_core_sci_sm",
+                task="ner",
                 path=None,
-                kwargs={"task": "ner"},
+                kwargs={},
             )
         )
         mock_spacy_nlp.return_value.assert_called_once()
@@ -67,7 +68,7 @@ def test_full_coding_pipeline_integration(mock_spacy_nlp, test_cda_request):
         "healthchain.pipeline.mixins.ModelRoutingMixin.get_model_component",
         mock_spacy_nlp,
     ):
-        pipeline = MedicalCodingPipeline.load(
+        pipeline = MedicalCodingPipeline.from_local_model(
             "./spacy/path/to/production/model", source="spacy"
         )
 

tests/pipeline/prebuilt/test_summarization.py

@@ -60,6 +60,7 @@ def test_summarization_pipeline(
             source=ModelSource.HUGGINGFACE.value,
             task="summarization",
             template=pipeline._output_template,
+            template_path=pipeline._output_template_path,
             delimiter="\n",
         )
 
@@ -90,22 +91,28 @@ def test_summarization_pipeline(
         assert "card-creation" in pipeline._stages
 
 
-def test_full_summarization_pipeline_integration(mock_hf_transformer, test_cds_request):
+def test_full_summarization_pipeline_integration(
+    mock_hf_transformer, test_cds_request, tmp_path
+):
     # Use mock LLM object for now
     with patch(
         "healthchain.pipeline.mixins.ModelRoutingMixin.get_model_component",
         mock_hf_transformer,
     ):
-        template = """
-    {
-        "summary": "This is a test summary",
-        "indicator": "warning",
-        "source": {{ default_source | tojson }},
-        "detail": "{{ model_output }}"
-    }
-    """
-        pipeline = SummarizationPipeline.load(
-            "llama3", source="huggingface", template=template
+        # Create a temporary template file
+        template_file = tmp_path / "card_template.json"
+        template_content = """
+        {
+            "summary": "This is a test summary",
+            "indicator": "warning",
+            "source": {{ default_source | tojson }},
+            "detail": "{{ model_output }}"
+        }
+        """
+        template_file.write_text(template_content)
+
+        pipeline = SummarizationPipeline.from_model_id(
+            "llama3", source="huggingface", template_path=template_file
         )
 
         cds_response = pipeline(test_cds_request)

tests/pipeline/test_pipeline.py

@@ -257,7 +257,7 @@ def test_pipeline_class_and_representation(mock_basic_pipeline):
     assert "comp1" in repr_string
     assert "comp2" in repr_string
 
-    loaded_pipeline = Pipeline.load("dummy_path")
+    loaded_pipeline = Pipeline.from_local_model("dummy_path", source="spacy")
     assert isinstance(loaded_pipeline, Pipeline)