Merge branch 'main' into api-enhanced-algo

.github/workflows/test.yaml

@@ -14,7 +14,7 @@ on:
 
 
 env:
-  TEST_RUNNER_PYTHON_VERSION: 3.9
+  TEST_RUNNER_PYTHON_VERSION: 3.11
 
 jobs:
   postgres-tests:

containers/alerts/Dockerfile

@@ -1,7 +1,11 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
 WORKDIR /code
 
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y git
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 

containers/alerts/requirements.txt

@@ -3,9 +3,9 @@ azure-communication-phonenumbers
 azure-communication-sms
 azure-identity
 typing_extensions==4.5.0
-pydantic==1.9.0
-fastapi==0.95.0
-phdi
+pydantic==1.10.9
+fastapi==0.96.0
+phdi @ git+https://github.com/CDCgov/phdi@updatepython
 uvicorn
 httpx
 slack_sdk

containers/fhir-converter/requirements.txt

@@ -6,10 +6,10 @@ charset-normalizer==2.1.0
 click==8.1.3
 dnspython==2.2.1
 email-validator==1.2.1
-fastapi==0.92.0
+fastapi==0.96.0
 h11==0.13.0
 httpcore==0.17.0
-httptools==0.4.0
+httptools==0.5.0
 httpx==0.24.0
 idna==3.3
 iniconfig==1.1.1
@@ -20,7 +20,7 @@ orjson==3.7.11
 packaging==21.3
 pluggy==1.0.0
 py==1.11.0
-pydantic==1.9.1
+pydantic==1.10.9
 pyparsing==3.0.9
 pytest==7.1.2
 python-dotenv==0.20.0
@@ -29,13 +29,13 @@ PyYAML==6.0
 requests==2.28.1
 six==1.16.0
 sniffio==1.2.0
-starlette==0.25.0
+starlette==0.27.0
 tomli==2.0.1
 typing_extensions==4.3.0
 ujson==5.4.0
 urllib3==1.26.11
 uvicorn==0.17.6
-uvloop==0.16.0
+uvloop==0.17.0
 watchgod==0.8.2
 websockets==10.3
 uuid

containers/ingestion/Dockerfile

@@ -1,7 +1,11 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
 WORKDIR /code
 
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y git
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 

containers/ingestion/requirements.txt

@@ -1,6 +1,6 @@
-typing_extensions==4.5.0
-pydantic==1.9.0
-fastapi==0.95.0
-phdi
+typing_extensions==4.6.3
+pydantic==1.10.9
+fastapi==0.96.0
+phdi @ git+https://github.com/CDCgov/phdi@updatepython
 uvicorn
 httpx

containers/message-parser/Dockerfile

@@ -1,7 +1,11 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
 WORKDIR /code
 
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y git
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 

containers/message-parser/requirements.txt

@@ -1,7 +1,7 @@
 typing_extensions==4.5.0
-pydantic==1.9.0
-fastapi==0.95.0
-phdi
+pydantic==1.10.9
+fastapi==0.96.0
+phdi @ git+https://github.com/CDCgov/phdi@updatepython
 uvicorn
 httpx
 pytest

containers/record-linkage/Dockerfile

@@ -1,11 +1,11 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
 WORKDIR /code
 
 RUN apt-get update && \
     apt-get upgrade -y && \
     apt-get install -y git
-    
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 

containers/record-linkage/requirements.txt

@@ -1,7 +1,7 @@
 typing_extensions==4.5.0
 uvicorn
-pydantic==1.9.0
-fastapi==0.95.0
-phdi @ git+https://github.com/CDCgov/phdi@main
+pydantic==1.10.9
+fastapi==0.96.0
+phdi @ git+https://github.com/CDCgov/phdi@updatepython
 httpx
 pathlib

containers/tabulation/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
 WORKDIR /code
 
@@ -8,6 +8,8 @@ RUN apt-get -y update && \
     apt-get upgrade -y && \
     apt-get -y install gcc
 
+RUN apt-get install -y git
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 

containers/tabulation/requirements.txt

@@ -1,7 +1,7 @@
 typing_extensions==4.5.0
-pydantic==1.9.0
-fastapi==0.95.0
-phdi
+pydantic==1.10.9
+fastapi==0.96.0
+phdi @ git+https://github.com/CDCgov/phdi@updatepython
 uvicorn
 httpx
 pytest

containers/validation/Dockerfile

@@ -1,7 +1,11 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
 WORKDIR /code
 
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y git
+
 COPY ./requirements.txt /code/requirements.txt
 RUN pip install -r requirements.txt
 

containers/validation/requirements.txt

@@ -1,7 +1,7 @@
 typing_extensions==4.5.0
-pydantic==1.9.0
-fastapi==0.95.0
-phdi
+pydantic==1.10.9
+fastapi==0.96.0
+phdi @ git+https://github.com/CDCgov/phdi@updatepython
 uvicorn
 httpx
 pytest

phdi/linkage/link.py

@@ -949,12 +949,15 @@ def read_linkage_config(config_file: pathlib.Path) -> List[dict]:
       various parts of linkage pass function.
     """
     try:
-        algo_config = json.load(open(config_file))
-        # Need to convert function keys back to column indices, since
-        # JSON serializes dict keys as strings
-        for rl_pass in algo_config.get("algorithm"):
-            rl_pass["funcs"] = {int(col): f for (col, f) in rl_pass["funcs"].items()}
-        return algo_config.get("algorithm", [])
+        with open(config_file) as f:
+            algo_config = json.load(f)
+            # Need to convert function keys back to column indices, since
+            # JSON serializes dict keys as strings
+            for rl_pass in algo_config.get("algorithm"):
+                rl_pass["funcs"] = {
+                    int(col): f for (col, f) in rl_pass["funcs"].items()
+                }
+            return algo_config.get("algorithm", [])
     except FileNotFoundError:
         raise FileNotFoundError(f"No file exists at path {config_file}.")
     except json.decoder.JSONDecodeError as e: