Initial commit

.gitignore

+.*
+!.gitignore
+!.gitlab-ci.yml
+_*
+!__init__.py
+!__main__.py

.gitlab-ci.yml

+stages:
+- prerun
+- test
+- deploy
+
+variables:
+  POSTGRES_HOST: postgres
+  POSTGRES_DB: postgres
+  POSTGRES_USER: postgres
+  POSTGRES_PASSWORD: ""
+  SAMPLEDB_SQLALCHEMY_DATABASE_URI: "postgresql+psycopg2://postgres:@postgres:5432/postgres"
+  POSTGRES_HOST_AUTH_METHOD: trust
+
+tag-type-check:
+  stage: prerun
+  image: busybox
+  only:
+    - tags
+  script:
+    # stop pipelines for lightweight tags
+    - test `git cat-file -t $CI_COMMIT_TAG` = "tag"
+
+analyze:
+  stage: test
+  image: python:3
+  script:
+    # install static analysis dependencies
+    - python3 -m pip install pycodestyle pyflakes
+    # run static analysis tools
+    - python3 -m pycodestyle --ignore=E402,E501,W504 qcodes_sampledb_import
+    - python3 -m pyflakes qcodes_sampledb_import
+
+test:
+  stage: test
+  image: ubuntu:18.04
+  services:
+    - postgres:12
+  script:
+    - apt-get update
+    # set up Python 3
+    - apt-get install -y git python3-pip libpangocairo-1.0-0
+    # install main dependencies
+    - python3 -m pip install -r requirements.txt
+    # install additional testing dependencies
+    - python3 -m pip install pytest sampledb
+    - export SAMPLEDB_FILE_STORAGE_PATH=${CI_PROJECT_DIR}/test_files/
+    # run tests and gather coverage data
+    - python3 -m pytest -x --cov=qcodes_sampledb_import/ --junitxml=pytest.xml tests
+  artifacts:
+    reports:
+      junit: pytest.xml
+
+documentation:
+  stage: test
+  image: python:3
+  script:
+    # install main dependencies
+    - python3 -m pip install -r requirements.txt
+    # install additional documentation dependencies
+    - python3 -m pip install sphinx sphinxcontrib-httpdomain vcversioner
+    # build documentation
+    - python3 -m sphinx -b html docs/ build_documentation/
+  artifacts:
+    paths:
+    - build_documentation
+
+pages:
+  stage: deploy
+  image: busybox
+  only:
+    - master
+    - tags
+  script:
+    # allow GitLab Pages to deploy the artifacts from the documentation job
+    - mv build_documentation public
+  artifacts:
+    paths:
+    - public
+    expire_in: 1 day
+
+deploy-to-pypi:
+  stage: deploy
+  image: python:3
+  only:
+    - tags@Scientific-IT-Systems/qcodes-sampledb-import
+  script:
+    # install packaging dependencies
+    - python3 -m pip install setuptools wheel twine
+    # build sdist
+    - python3 setup.py sdist
+    # deploy sdist to PyPI for version tags
+    - if echo "$CI_COMMIT_TAG" | grep -Eq '^v[0-9]+\.[0-9]+\.[0-9]+$'; then
+        export VERSION=`echo "$CI_COMMIT_TAG" | sed 's/^v//'`;
+        python3 -m twine upload dist/qcodes-sampledb-import-$VERSION.tar.gz;
+      fi

LICENSE

+MIT License
+
+Copyright (c) 2021 PGI / JCNS Scientific IT-Systems
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

+# QCoDeS SampleDB Import
+
+[![MIT license](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.md)
+
+A tool for importing data from QCoDeS into SampleDB.

docs/changelog.rst

+Changelog
+=========
+
+Version 0.1
+-----------
+
+Currently in development.
+
+- Set up basic project structure
\ No newline at end of file

docs/conf.py

+# coding: utf-8
+
+import os
+import sys
+import vcversioner
+import datetime
+
+base_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+sys.path.insert(0, base_dir)
+
+# Project information
+
+project = 'QCoDeS-SampleDB-Import'
+description = 'A tool for importing data from QCoDeS into SampleDB.'
+copyright = '{}, PGI / JCNS Scientific IT-Systems'.format(datetime.date.today().year)
+author = 'Florian Rhiem'
+contact_email = 'f.rhiem@fz-juelich.de'
+imprint = 'https://pgi-jcns.fz-juelich.de/portal/pages/imprint.html'
+
+# The full version, including alpha/beta/rc tags
+release = vcversioner.find_version(root=base_dir).version
+
+# The short X.Y version
+version = '.'.join(release.split('.', 2)[:2])
+
+# General configuration
+
+source_suffix = '.rst'
+
+master_doc = 'index'
+
+exclude_patterns = []
+
+language = None
+
+templates_path = ['templates']
+
+pygments_style = None
+
+extensions = [
+    'sphinx.ext.todo',
+    'sphinx.ext.autodoc',
+    'sphinxcontrib.httpdomain',
+]
+
+todo_include_todos = False
+
+# Options for HTML output
+
+html_theme = 'alabaster'
+html_static_path = ['static']
+html_show_sourcelink = False
+
+# Options for Alabaster theme
+html_theme_options = {
+    'logo_text_align': 'center',
+    'description': description,
+    'font_family': "'Lato', 'Helvetica Neue', 'Arial', sans-serif",
+    'font_size': '16px',
+    'head_font_family': "'Lato', 'Helvetica Neue', 'Arial', sans-serif",
+    'body_text_align': 'justify',
+    'show_powered_by': False,
+    'extra_nav_links': {
+        'Source Code': 'https://iffgit.fz-juelich.de/Scientific-IT-Systems/qcodes-sampledb-import/',
+        'Issues': 'https://iffgit.fz-juelich.de/Scientific-IT-Systems/qcodes-sampledb-import/-/issues',
+        'Contact': 'mailto:{}'.format(contact_email),
+        'Imprint': imprint,
+        'PGI/JCNS-TA': 'https://pgi-jcns.fz-juelich.de',
+    }
+}
+
+# Options for other output methods
+
+htmlhelp_basename = '{}doc'.format(project)
+
+latex_elements = {}
+latex_documents = [
+    (master_doc, '{}.tex'.format(project), '{} Documentation'.format(project),
+     author, 'manual'),
+]
+
+man_pages = [
+    (master_doc, project.lower(), '{} Documentation'.format(project),
+     [author], 1)
+]
+
+texinfo_documents = [
+    (master_doc, project, '{} Documentation'.format(project),
+     author, project, description,
+     'Miscellaneous'),
+]
+
+epub_title = project
+epub_exclude_files = ['search.html']
+
+
+def setup(app):
+    app.add_css_file('css/custom.css')

docs/index.rst

+QCoDeS-SampleDB-Import
+======================
+
+.. toctree::
+    :hidden:
+    :maxdepth: 2
+
+    changelog.rst

qcodes_sampledb_import/__init__.py

+# coding: utf-8
+"""
+
+"""

qcodes_sampledb_import/__main__.py

+# coding: utf-8
+"""
+A tool for importing research data from QCoDeS into SampleDB
+
+Usage: python -m qcodes_sampledb_import
+"""
+
+import sys
+import typing
+
+
+def main(argv: typing.List[str]) -> int:
+    if len(argv) > 1:
+        print(__doc__)
+        return 1
+    # TODO: implement functionality
+    return 0
+
+
+if __name__ == '__main__':
+    exit(main(sys.argv))

qcodes_sampledb_import/version.py

+# coding: utf-8
+"""
+This file should only contain the definition of the __version__ variable.
+
+It may be read by multiple other files, e.g. setup.py.
+"""
+
+__version__ = '0.0.0'

requirements.txt

+requests>=2.25.1

requirements_dev.txt

+pytest
+sampledb
+sphinx
+sphinxcontrib-httpdomain
+vcversioner

setup.py

+# coding: utf-8
+"""
+
+"""
+
+import importlib.util
+from setuptools import setup, find_packages
+import os.path
+
+setup_directory = os.path.abspath(os.path.dirname(__file__))
+
+with open(os.path.join(setup_directory, 'README.md')) as readme_file:
+    long_description = readme_file.read()
+
+with open(os.path.join(setup_directory, 'requirements.txt')) as requirements_file:
+    requirements = requirements_file.readlines()
+
+version_file_path = os.path.join(setup_directory, 'qcodes_sampledb_import', 'version.py')
+spec = importlib.util.spec_from_file_location("version", version_file_path)
+version = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(version)
+
+
+setup(
+    name='qcodes_sampledb_import',
+    version=version.__version__,
+    description='A tool for importing data from QCoDeS into SampleDB.',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    url='https://iffgit.fz-juelich.de/Scientific-IT-Systems/qcodes-sampledb-import',
+    author='Florian Rhiem',
+    author_email='f.rhiem@fz-juelich.de',
+    license='MIT',
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Developers',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3',
+        'Topic :: Scientific/Engineering',
+    ],
+    packages=find_packages(exclude=['tests']),
+    install_requires=requirements
+)

tests/__init__.py

+# coding: utf-8
+"""
+
+"""
+
+__author__ = 'Florian Rhiem <f.rhiem@fz-juelich.de>'

tests/conftest.py

+# coding: utf-8
+"""
+Setup and configuration for tests
+"""
+
+import copy
+import logging
+import os
+import random
+import secrets
+import threading
+import time
+
+import flask
+import pytest
+import requests
+import sqlalchemy
+
+import sampledb
+import sampledb.utils
+import sampledb.config
+
+# SampleDB configuration
+sampledb.config.MAIL_SUPPRESS_SEND = True
+sampledb.config.TEMPLATES_AUTO_RELOAD = True
+
+sampledb.config.SQLALCHEMY_DATABASE_URI = 'postgresql+psycopg2://postgres:@localhost:5432/postgres'
+sampledb.config.MAIL_SENDER = 'sampledb@example.com'
+sampledb.config.MAIL_SERVER = 'mail.example.com'
+sampledb.config.CONTACT_EMAIL = 'sampledb@example.com'
+sampledb.config.LDAP_NAME = 'LDAP'
+
+# restore possibly overridden configuration data from environment variables
+sampledb.config.use_environment_configuration(env_prefix='SAMPLEDB_')
+
+
+def create_flask_server(app):
+    if not getattr(app, 'has_shutdown_route', False):
+        @app.route('/shutdown', methods=['POST'])
+        def shutdown():
+            func = flask.request.environ.get('werkzeug.server.shutdown')
+            if func is None:
+                raise RuntimeError('Not running with the Werkzeug Server')
+            func()
+            return 'Server shutting down...'
+        app.has_shutdown_route = True
+
+    port = random.randint(10000, 20000)
+    server_thread = threading.Thread(target=lambda: app.run(port=port, debug=True, use_reloader=False), daemon=True)
+    server_thread.start()
+    server_thread.app = app
+    server_thread.initial_config = copy.deepcopy(server_thread.app.config)
+    server_thread.base_url = 'http://localhost:{0}/'.format(port)
+    server_thread.api_url = server_thread.base_url + 'api/'
+    # short delay to allow the web server to start
+    time.sleep(0.1)
+    yield server_thread
+    # restore initial configuration
+    server_thread.app.config = server_thread.initial_config
+    r = requests.post(server_thread.base_url + 'shutdown')
+    assert r.status_code == 200
+    server_thread.join()
+
+
+@pytest.fixture(scope='session')
+def flask_server():
+    app = create_app()
+    # empty the database first, to ensure all tests rebuild it before use
+    sampledb.utils.empty_database(sqlalchemy.create_engine(sampledb.config.SQLALCHEMY_DATABASE_URI), only_delete=True)
+    yield from create_flask_server(app)
+
+
+def create_app():
+    logging.getLogger('flask.app').setLevel(logging.WARNING)
+    os.environ['FLASK_ENV'] = 'development'
+    os.environ['FLASK_TESTING'] = 'True'
+    sampledb.utils.empty_database(sqlalchemy.create_engine(sampledb.config.SQLALCHEMY_DATABASE_URI), only_delete=True)
+    sampledb_app = sampledb.create_app()
+    return sampledb_app
+
+
+@pytest.fixture
+def app(flask_server):
+    app = flask_server.app
+    # reset config and database before each test
+    app.config = copy.deepcopy(flask_server.initial_config)
+    sampledb.utils.empty_database(sqlalchemy.create_engine(sampledb.config.SQLALCHEMY_DATABASE_URI), only_delete=True)
+    sampledb.setup_database(app)
+    return app
+
+
+@pytest.fixture(autouse=True)
+def app_context(app):
+    with app.app_context():
+        # yield to keep the app context active until the test is done
+        yield None
+
+
+@pytest.fixture
+def api_token_user(flask_server):
+    with flask_server.app.app_context():
+        user = sampledb.logic.users.create_user(name="Test User", email="example@example.com", type=sampledb.models.UserType.PERSON)
+        assert user.id is not None
+        sampledb.logic.authentication.add_other_authentication(user.id, 'username', 'password')
+        api_token = secrets.token_hex(32)
+        sampledb.logic.authentication.add_api_token(user.id, api_token, "Test API Token")
+    return api_token, user
+
+
+@pytest.fixture
+def api_token_headers(api_token_user):
+    api_token, _ = api_token_user
+    return {
+        'Authorization': 'Bearer ' + api_token
+    }

tests/test_example.py

+# coding: utf-8
+"""
+These tests are examples using the SampleDB API and the CLI.
+"""
+
+import requests
+import qcodes_sampledb_import.__main__ as entrypoint
+
+
+def test_sampledb_api(flask_server, api_token_headers):
+    r = requests.get(
+        flask_server.base_url + 'api/v1/objects/',
+        headers=api_token_headers
+    )
+    assert r.status_code == 200
+    assert r.json() == []
+
+
+def test_cli():
+    assert entrypoint.main([entrypoint.__file__]) == 0
+    assert entrypoint.main([entrypoint.__file__, "..."]) == 1

version.txt

+v0.0.0-0-placeholder