Merge pull request #65 from pennsignals/flowsheets

Add flowsheets

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
   - id: check-added-large-files
   - id: check-case-conflict
   - id: check-docstring-first
-  - id: check-executables-have-shebangs
+  - id: check-json
   - id: check-merge-conflict
   - id: check-toml
   - id: check-symlinks
@@ -26,22 +26,25 @@ repos:
   hooks:
   - id: black
     language_version: python3.9
+    types: [python]
 - repo: https://github.com/pycqa/pylint
   rev: v2.12.2
   hooks:
   - id: pylint
     language: system
+    types: [python]
 - repo: https://gitlab.com/pycqa/flake8
   rev: 4.0.1
   hooks:
   - id: flake8
     language: system
-# - repo: https://github.com/python/mypy
+    types: [python]
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v0.930
   hooks:
   - id: mypy
     language: system
+    types: [python]
 - repo: local
   hooks:
   - id: pytest

docker-compose.yml

@@ -30,59 +30,12 @@ services:
     build:
       context: .
       target: test
-    depends_on:
-    - postgres
-    - notifier
-    - verifier
-    - epic
     environment:
-    - CONFIG=/local/test.yaml
-    - ENV=/local/docker.env
+    - CONFIG=./local/test.yaml
+    - ENV=./secrets/example.env
     volumes:
     - ./assets:/assets
+    - ./gold:/gold
     - ./local:/local
-
-  notifier:
-    build:
-      context: .
-      target: epic
-    command: epic.notify
-    depends_on:
-    - epic
-    - postgres
-    environment:
-    - CONFIG=/local/notifier.yaml
-    - ENV=/local/docker.env
-    volumes:
-    - ./assets:/assets
-    - ./local:/local
-
-  verifier:
-    build:
-      context: .
-      target: epic
-    command: epic.verify
-    depends_on:
-    - epic
-    - postgres
-    environment:
-    - CONFIG=/local/verifier.yaml
-    - ENV=/local/docker.env
-    volumes:
-    - ./assets:/assets
-    - ./local:/local
-
-  epic:
-    build:
-      context: .
-      target: epic
-    environment:
-    - CONFIG=/local/epic.yaml
-    - ENV=/local/docker.env
-    expose:
-    - "80"
-    ports:
-    - "80:80"
-    restart: always
-    volumes:
-    - ./local:/local
+    - ./model:/model
+    - ./secrets:/secrets

dockerfile

@@ -26,22 +26,15 @@ RUN \
     apt-get -qq autoremove -y --purge && \
     rm -rf /var/lib/apt/lists/*
 
-FROM python:3.9.9-slim-bullseye as epic
-LABEL name="epic"
-WORKDIR /tmp
-ENV FREETDS /etc/freetds
-ENV PATH /root/.local/bin:$PATH
-COPY --from=build /root/.local /root/.local
-COPY --from=build /tmp/assets /tmp/assets
-COPY --from=build /usr/bin/tini /usr/bin
-ENTRYPOINT ["/usr/bin/tini", "--"]
-CMD ["epic"]
-
 FROM build as test
 ARG IFLAGS
 LABEL name="dsdk.test"
 WORKDIR /tmp
 RUN \
-    pip install ${IFLAGS} ".[all]"
+    pip install ${IFLAGS} ".[all]" && \
+    ln -s /local ./local && \
+    ln -s /secrets ./secrets && \
+    ln -s /model ./model && \
+    ln -s /gold ./gold
 ENTRYPOINT [ "/usr/bin/tini", "--" ]
 CMD [ "pre-commit", "run", "--all-files" ]

local/.gitignore

@@ -1,6 +1,5 @@
 *
 !.gitignore
 !configuration.yaml
-!notifier.yaml
-!verifier.yaml
-!epic.yaml
+!docker.yaml
+!test.yaml

local/configuration.yaml

@@ -1,6 +1,18 @@
+!example
+flowsheets: !flowsheets
+  client_id: ${EPIC_CLIENT_ID}
+  cookie: ${EPIC_COOKIE}
+  flowsheet_id: ${EPIC_FLOWSHEET_ID}
+  flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
+  password: ${EPIC_PASSWORD}
+  url: ${EPIC_URL}api/epic/2011/clinical/patient/addflowsheetvalue/flowsheetvalue
+  username: ${EPIC_USERNAME}
 postgres: !postgres
   database: ${POSTGRES_DATABASE}
-  host: ${POSTRES_HOST}
+  host: ${POSTGRES_HOST}
   password: ${POSTGRES_PASSWORD}
-  port: 5432
+  port: ${POSTGRES_PORT}
+  schema: example
+  sql: null
   username: ${POSTGRES_USERNAME}
+time_zone: America/New_York

local/test.yaml

@@ -0,0 +1,20 @@
+!example
+as_of: 2019-09-18 17:19:23.873398+00
+gold: ./predict/gold/gold.pkl
+flowsheets: !flowsheets
+  client_id: ${EPIC_CLIENT_ID}
+  cookie: ${EPIC_COOKIE}
+  flowsheet_id: ${EPIC_FLOWSHEET_ID}
+  flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
+  password: ${EPIC_PASSWORD}
+  url: ${EPIC_URL}api/epic/2011/clinical/patient/addflowsheetvalue/flowsheetvalue
+  username: ${EPIC_USERNAME}
+postgres: !postgres
+  database: ${POSTGRES_DATABASE}
+  host: ${POSTGRES_HOST}
+  password: ${POSTGRES_PASSWORD}
+  port: ${POSTGRES_PORT}
+  schema: example
+  sql: null
+  username: ${POSTGRES_USERNAME}
+time_zone: America/New_York

secrets/.gitignore

@@ -1,3 +1,3 @@
 *
 !.gitignore
-!docker.env
+!example.env

secrets/example.env

@@ -0,0 +1,13 @@
+EPIC_CLIENT_ID=00000000-0000-0000-0000-000000000000
+EPIC_COOKIE=ASP.NET_SessionId=000000000000000000000000
+EPIC_FLOWSHEET_ID=0000000000
+EPIC_FLOWSHEET_TEMPLATE_ID=0000000000
+EPIC_PASSWORD=password
+EPIC_URL=https://interconnectbgprod.uphs.upenn.edu/interconnect-prd-web/
+EPIC_USERNAME=epic
+EPIC_USER_ID=PENNSIGNALS
+POSTGRES_DATABASE=test
+POSTGRES_HOST=postgres
+POSTGRES_PASSWORD=password
+POSTGRES_PORT=5432
+POSTGRES_USERNAME=postgres

setup.py

@@ -51,18 +51,10 @@
     "types-pymssql",
     "types-pyyaml",
     "types-requests",
+    "vcrpy",
 )
 
 setup(
-    entry_points={
-        "console_scripts": [
-            "epic = dsdk.epic:Server.main"
-            "epic.notify = dsdk.epic:Notifier.main",
-            "epic.verify = dsdk.epic:Verifier.main",
-            "epic.notify.api.test = dsdk.epic:Notifier.test",
-            "epic.verify.api.test = dsdk.epic:Verifier.test",
-        ]
-    },
     extras_require={
         "all": (PSYCOPG2_REQUIRES + PYMSSQL_REQUIRES + TEST_REQUIRES),
         "psycopg2": PSYCOPG2_REQUIRES,

src/dsdk/__init__.py

@@ -2,6 +2,8 @@
 """Data Science Deployment Kit."""
 
 from .asset import Asset
+from .flowsheet import Mixin as FlowsheetMixin
+from .flowsheet import Flowsheet
 from .interval import Interval
 from .model import Mixin as ModelMixin
 from .model import Model
@@ -28,6 +30,8 @@
     "Batch",
     "Delegate",
     "Interval",
+    "Flowsheet",
+    "FlowsheetMixin",
     "Model",
     "ModelMixin",
     "MssqlMixin",