Merge pull request #62 from pennsignals/epic

Epic API tests

.pre-commit-config.yaml

@@ -6,31 +6,28 @@ repos:
   - 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
-  - id: check-xml
-  - id: check-yaml
   - id: end-of-file-fixer
   - id: fix-encoding-pragma
   - id: mixed-line-ending
-  - id: requirements-txt-fixer
   - id: trailing-whitespace
 - repo: http://github.com/pre-commit/pygrep-hooks
-  rev: v1.4.2
+  rev: v1.9.0
   hooks:
   - id: python-check-blanket-noqa
+  - id: python-check-blanket-type-ignore
+  - id: python-no-eval
+  - id: python-no-log-warn
   - id: python-use-type-annotations
-  - id: rst-backticks
-# - repo: https://github.com/pre-commit/mirrors-isort
-- repo: https://github.com/timothycrosley/isort
-  rev: 4.3.21-2
+- repo: https://github.com/pycqa/isort
+  rev: 5.8.0
   hooks:
   - id: isort
     additional_dependencies: [toml]
 - repo: https://github.com/psf/black
-  rev: 19.10b0
+  rev: 21.7b0
   hooks:
   - id: black
     language_version: python3.9

assets/postgres/epic/notifications/channel.sql

@@ -0,0 +1 @@
+listen example.epic_notifications

assets/postgres/epic/notifications/errors/insert.sql

@@ -0,0 +1,10 @@
+insert into epic_notification_errors (
+    prediction_id,
+    name,
+    description
+)
+select
+    %(prediction_id)s,
+    %(name)s,
+    %(description)s
+returning *

assets/postgres/epic/notifications/insert.sql

@@ -0,0 +1,6 @@
+insert into epic_notifications (
+    prediction_id
+)
+select
+    %(prediction_id)s
+returning *

assets/postgres/epic/notifications/recent.sql

@@ -0,0 +1,31 @@
+with args as (
+    select
+        cast(%(notification_id)s as int) as notification_id
+)
+select
+    n.id
+    p.id as prediction_id,
+    p.run_id,
+    p.csn,
+    p.empi,
+    p.score,
+    r.as_of
+from
+    args
+    join runs as r
+        upper(r.interval) != 'infinity'
+    join predictions as p on
+        p.run_id = r.id
+    join epic_notifications as n on
+        n.prediction_id = p.id
+        and n.id <= args.notification_id
+    left join epic_verifcations as v on
+        v.notification_id = n.id
+    left join epic_verification_errors as e on
+        e.notification_id = n.id
+        and e.acknowledged_on is null
+where
+    v.id is null
+    and e.id is null
+order by
+    r.id, p.id

assets/postgres/epic/notifications/recover.sql

@@ -0,0 +1,24 @@
+select
+    n.id,
+    p.id as prediction_id,
+    p.csn,
+    p.empi,
+    p.score,
+    r.as_of
+from
+    runs as r
+    join predictions as p on
+        p.run_id = r.id
+        and upper(r.interval) != 'infinity'
+    join epic_notifications as n on
+        n.prediction_id = p.id
+    left join epic_verifications as v on
+        v.notification_id = n.id
+    left join epic_verification_errors as e on
+        e.notification_id = n.id
+        and e.acknowledged_on is null
+where
+    v.id is null
+    and e.id is null
+order by
+    p.id, n.id

assets/postgres/epic/verifications/errors/insert.sql

@@ -0,0 +1,10 @@
+insert into epic_verification_errors (
+    notification_id,
+    name,
+    description,
+)
+select
+    %(notification_id)s,
+    %(name)s,
+    %(description)s
+returning *

assets/postgres/epic/verifications/insert.sql

@@ -0,0 +1,6 @@
+insert into epic_verifications (
+    notification_id
+)
+select
+    %(notification_id)s
+returning *

assets/postgres/predictions/listen.sql

@@ -0,0 +1 @@
+listen example.predictions

assets/postgres/predictions/recent.sql

@@ -0,0 +1,28 @@
+with args as (
+    select
+        cast(%(prediction_id)s as int) as prediction_id
+)
+select
+    p.id,
+    p.run_id,
+    p.csn,
+    p.empi,
+    p.score,
+    r.as_of
+from
+    args
+    join runs as r
+        upper(r.interval) != 'infinity'
+    join predictions as p on
+        p.id <= args.prediction_id
+        and p.run_id = r.id
+    left join epic_notifications as n on
+        n.prediction_id = p.id
+    left join epic_notification_errors as e on
+        e.prediction_id = p.id
+        and e.acknowledged_on is null
+where
+    n.id is null
+    and e.id is null
+order by
+    r.id, p.id

assets/postgres/predictions/recover.sql

@@ -0,0 +1,22 @@
+select
+    p.id,
+    p.run_id,
+    p.csn,
+    p.empi,
+    p.score,
+    r.as_of
+from
+    runs as r
+    join predictions as p on
+        p.run_id = r.id
+        and upper(r.interval) != 'infinity'
+    left join epic_notifications as n on
+        n.prediction_id = p.prediction_id
+    left join epic_notification_errors as e on
+        e.prediction_id = p.prediction_id
+        and e.acknowledged_on is null
+where
+    n.id is null
+    and e.id is null
+order by
+    r.id, p.id

assets/postgres/schema.sql

@@ -0,0 +1 @@
+set search_path = example;

buster.dockerfile

@@ -1,8 +1,8 @@
 ARG IFLAGS="--quiet --no-cache-dir --user"
 
-FROM python:3.9.4-slim-buster as build
+FROM python:3.9.6-slim-buster as build
 ARG IFLAGS
-WORKDIR /root
+WORKDIR /tmp
 ENV PATH /root/.local/bin:$PATH
 ENV TINI_VERSION v0.19.0
 ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
@@ -14,21 +14,31 @@ COPY pyproject.toml .
 COPY .pre-commit-config.yaml .
 COPY .git ./.git
 COPY src ./src
-COPY sql ./sql
+COPY assets ./assets
 COPY test ./test
 RUN \
     chmod +x /usr/bin/tini && \
     apt-get -qq update --fix-missing && \
-    apt-get -qq install -y --no-install-recommends git > /dev/null && \
+    apt-get -qq install -y --no-install-recommends git libyaml-dev > /dev/null && \
     pip install ${IFLAGS} "." && \
     apt-get -qq clean && \
     apt-get -qq autoremove -y --purge && \
     rm -rf /var/lib/apt/lists/*
 
+FROM python:3.9.6-slim-buster as epic
+LABEL name="epic"
+WORKDIR /tmp
+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 /root
+WORKDIR /tmp
 RUN \
     pip install ${IFLAGS} ".[all]"
 ENTRYPOINT [ "/usr/bin/tini", "--" ]

docker-compose.yml

@@ -29,11 +29,57 @@ services:
       target: test
     depends_on:
     - postgres
+    - notifier
+    - verifier
+    - epic
     environment:
-    - POSTGRES_HOST=postgres
-    - POSTGRES_USERNAME=postgres
-    - POSTGRES_PASSWORD=postgres
-    - POSTGRES_DATABASE=test
-    - POSTGRES_PORT=5432
+    - CONFIG=/local/test.yaml
+    - ENV=/local/docker.env
+    volumes:
+    - ./assets:/assets
+    - ./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:
-    - ./sql:/sql
+    - ./local:/local

local/.gitignore

@@ -1,2 +1,6 @@
 *
 !.gitignore
+!configuration.yaml
+!notifier.yaml
+!verifier.yaml
+!epic.yaml

local/configuration.yaml

@@ -0,0 +1,6 @@
+postgres: !postgres
+  database: ${POSTGRES_DATABASE}
+  host: ${POSTRES_HOST}
+  password: ${POSTGRES_PASSWORD}
+  port: 5432
+  username: ${POSTGRES_USERNAME}

local/epic.yaml

@@ -0,0 +1,4 @@
+!epic
+address: 0.0.0.0:80
+add_flowsheet_value_path: ${EPIC_ROOT}${EPIC_ADD_FLOWSHEET_VALUE_PATH}
+get_flowsheet_rows_path: ${EPIC_ROOT}${EPIC_GET_FLOWSHEET_ROWS_PATH}

local/notifier.yaml

@@ -0,0 +1,19 @@
+!epicnotifier
+client_id: ${EPIC_CLIENT_ID}
+cookie: ${EPIC_COOKIE}
+flowsheet_id: ${EPIC_FLOWSHEET_ID}
+flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
+password: ${EPIC_PASSWORD}
+postgres: !postgres
+  database: ${POSTGRES_DATABASE}
+  host: ${POSTGRES_HOST}
+  password: ${POSTGRES_PASSWORD}
+  port: 5432
+  sql: !asset
+    ext: .sql
+    path: ./assets/postgres
+  tables: []
+  username: ${POSTGRES_USERNAME}
+username: ${EPIC_USERNAME}
+user_id: ${EPIC_USER_ID}
+url: ${EPIC_URL}${EPIC_ROOT}${EPIC_ADD_FLOWSHEET_VALUE_PATH}

local/verifier.yaml

@@ -0,0 +1,19 @@
+!epicverifier
+client_id: ${EPIC_CLIENT_ID}
+cookie: ${EPIC_COOKIE}
+flowsheet_id: ${EPIC_FLOWSHEET_ID}
+flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
+password: ${EPIC_PASSWORD}
+postgres: !postgres
+  database: ${POSTGRES_DATABASE}
+  host: ${POSTGRES_HOST}
+  password: ${POSTGRES_PASSWORD}
+  port: 5432
+  sql: !asset
+    ext: .sql
+    path: ./assets/postgres
+  tables: []
+  username: ${POSTGRES_USERNAME}
+username: ${EPIC_USERNAME}
+user_id: ${EPIC_USER_ID}
+url: ${EPIC_URL}${EPIC_ROOT}${EPIC_GET_FLOWSHEET_ROWS_PATH}

postgres/dockerfile

@@ -1,4 +1,4 @@
-FROM timescale/timescaledb-postgis:latest-pg11 as postgres
+FROM timescale/timescaledb-postgis:latest-pg13 as postgres
 LABEL name=postgres
 COPY ./docker-entrypoint.sh /usr/local/bin/
 COPY ./sql/initdb.d/*.sql /docker-entrypoint-initdb.d/

postgres/sql/initdb.d/003.create.sql

@@ -1,5 +1,5 @@
 create extension if not exists btree_gist;
 
-create schema if not exists dsdk;
-grant usage on schema dsdk to public;
-grant create on schema dsdk to public;
+create schema if not exists example;
+grant usage on schema example to public;
+grant create on schema example to public;