add new files for containerization; still some work to do, but want to merge in tests first

.coveragerc

@@ -0,0 +1,44 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+omit =
+    */site-packages/*
+    */distutils/*
+    */test/*
+    */__init__.py
+    */setup.py
+source =
+    ner
+relative_files = True
+data_file = .coverage
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+omit =
+    */test/*
+    *test.py
+    */__init__.py
+    */setup.py
+
+ignore_errors = True
+
+[html]
+directory = reports
+
+[xml]
+output = reports/coverage.xml

.dockerignore

@@ -0,0 +1,100 @@
+/build_venv/
+/bamboo-specs/
+README.md
+*idea
+*egg-info
+*pycache*
+
+# Git
+.git
+.gitignore
+
+# CI
+.codeclimate.yml
+.travis.yml
+.taskcluster.yml
+
+# Docker
+docker-compose.yml
+.docker
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*/__pycache__/
+*/*/__pycache__/
+*/*/*/__pycache__/
+*.py[cod]
+*/*.py[cod]
+*/*/*.py[cod]
+*/*/*/*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Virtual environment
+.env/
+.venv/
+#venv/
+
+# PyCharm
+.idea
+
+# Python mode for VIM
+.ropeproject
+*/.ropeproject
+*/*/.ropeproject
+*/*/*/.ropeproject
+
+# Vim swap files
+*.swp
+*/*.swp
+*/*/*.swp
+*/*/*/*.swp

Dockerfile

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+ARG BASE_ROOT="nexus.iqser.com:5001/red/"
+ARG VERSION_TAG=latest
+
+FROM ${BASE_ROOT}ner-prediction-base:${VERSION_TAG}
+
+WORKDIR /app/service
+
+COPY ./src ./src
+COPY ner ./ner
+
+RUN python3 -m pip install -e .
+
+WORKDIR /app/service
+
+EXPOSE 5000
+EXPOSE 8080
+
+CMD ["python3", "src/run_service.py"]

Dockerfile_base

@@ -0,0 +1,25 @@
+FROM python:3.10 as builder1
+
+# Use a virtual environment.
+RUN python -m venv /app/venv
+ENV PATH="/app/venv/bin:$PATH"
+
+# Upgrade pip.
+RUN python -m pip install --upgrade pip
+
+# Make a directory for the service files and copy the service repo into the container.
+WORKDIR /app/service
+COPY . ./
+
+# Install dependencies.
+RUN python3 -m pip install -r requirements.txt
+
+# Make a new container and copy all relevant files over to filter out temporary files
+# produced during setup to reduce the final container's size.
+FROM python:3.10
+
+WORKDIR /app/
+COPY --from=builder1  /app .
+ENV PATH="/app/venv/bin:$PATH"
+
+WORKDIR /app/service

config.yaml

@@ -0,0 +1,9 @@
+device: cpu
+service:
+  logging_level: $LOGGING_LEVEL_ROOT|INFO # Logging level for log file messages
+  logfile_path: $LOGFILE_PATH|null  # Overwrites the default path for the service logfile (image_service/log.log)
+
+webserver:
+  host: $SERVER_HOST|"127.0.0.1"  # webserver address
+  port: $SERVER_PORT|5000  # webserver port
+  mode: $SERVER_MODE|production  # webserver mode: {development, production}

sonar-project.properties

@@ -0,0 +1,4 @@
+sonar.exclusions=bamboo-specs/**, venv/**, **/*.js, **/*.html, **/*.css, data/**
+sonar.c.file.suffixes=-
+sonar.cpp.file.suffixes=-
+sonar.objc.file.suffixes=-

src/run_service.py

@@ -0,0 +1,85 @@
+import argparse
+import json
+import logging
+"""
+from tkinter import W
+
+from flask import Flask, request, jsonify
+
+from ner.logging import logger
+from ner.predictor import Predictor
+from ner.utils.utils import extract_section_numbers2texts
+from ner.config import CONFIG
+from waitress import serve
+
+
+def suppress_user_warnings():
+    import warnings
+
+    warnings.filterwarnings("ignore")
+
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--warnings", action="store_true", default=False)
+    args = parser.parse_args()
+
+    return args
+
+
+def main(args):
+
+    if not args.warnings:
+        suppress_user_warnings()
+
+    run_server()
+
+
+def run_server():
+    def initialize_predictor():
+        predictor = Predictor()
+        return predictor
+
+    app = Flask(__name__)
+
+    @app.route("/", methods=["POST"])
+    def predict_request():
+        def inner():
+            data = request.data
+            logger.info(f"<3 Received data.")
+            section_text = json.loads(data)
+            section_numbers2texts = extract_section_numbers2texts(section_text)
+            logger.info(f"Processing data. <3")
+            predictions = predictor.predict(section_numbers2texts)
+
+            return jsonify({"result": predictions})
+
+        try:
+            return inner()
+        except Exception as err:
+            logger.warning("Analysis failed")
+            logger.exception(err)
+            resp = jsonify("Analysis failed")
+            resp.status_code = 500
+            return resp
+
+    @app.route("/status", methods=["GET"])
+    def status():
+        response = "OK"
+        return jsonify(response)
+
+    predictor = initialize_predictor()
+
+    logger.info("<3 Predictor ready.")
+
+    mode = CONFIG.webserver.mode
+    if mode == "development":
+        app.run(host=CONFIG.webserver.host, port=CONFIG.webserver.port, debug=True)
+    elif mode == "production":
+        serve(app, host=CONFIG.webserver.host, port=CONFIG.webserver.port)
+
+
+if __name__ == "__main__":
+    args = parse_args()
+    main(args)
+"""