First skeleton of hbp-spatial-backend

.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+# Defaults for every file
+[*]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.json]
+indent_size = 2
+
+# Makefiles must use tabs for indentation
+[Makefile]
+indent_style = tab

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+.pytest_cache/
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+coverage.xml
+*.cover
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Sphinx documentation
+docs/_build/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/

.travis.yml

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+language: python
+# The next two lines are here to fix build with Pyton 3.7, see
+# https://github.com/travis-ci/travis-ci/issues/9069#issuecomment-425720905
+sudo: required
+dist: xenial
+python:
+  - "3.5"
+  - "3.6"
+  - "3.7"
+install: pip install tox-travis
+script: tox

MANIFEST.in

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+include LICENCE.txt
+include .coveragerc
+include .editorconfig
+include *.ini
+include *.sh
+
+prune docker-aims
+prune docker-backend
+
+recursive-include tests *.py

docker-aims/Dockerfile

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+FROM ubuntu:16.04
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends --no-install-suggests \
+        libblitz0v5 \
+        libsigc++-2.0-0v5 \
+        libxml2 \
+        libqtcore4 \
+        zlib1g \
+        python2.7 \
+        python-sip \
+        libpython2.7 \
+        python-pip \
+        python-six \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# We need to use the same version of numpy as casa-dev:ubuntu-16.04
+# RUN pip install --disable-pip-version-check --no-cache-dir \
+#     numpy==1.13.1
+
+COPY install /usr/local
+RUN ldconfig
+
+# Make the BrainVISA Python packages visible to the system
+RUN mkdir -p /usr/local/lib/python2.7/dist-packages \
+    && cd /usr/local/lib/python2.7/dist-packages \
+    && ln -s ../../../python/* .

docker-aims/script.sh

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+# Run from the directory that contains this script (docker-aims)
+
+CASA_DISTRO_DIR=/volatile/bv/casa_distro_repo
+
+casa_distro \
+    -r "$CASA_DISTRO_DIR" \
+    create \
+    distro_name=aims \
+    distro_source=opensource \
+    branch=bug_fix \
+    system=ubuntu-16.04
+
+cat <<'EOF' > "$CASA_DISTRO_DIR"/aims/bug_fix_ubuntu-16.04/conf/bv_maker.cfg
+[ source $CASA_SRC ]
+  brainvisa brainvisa-cmake $CASA_BRANCH
+  brainvisa soma-base $CASA_BRANCH
+  brainvisa soma-io $CASA_BRANCH
+  brainvisa aims-free $CASA_BRANCH
+
+[ build $CASA_BUILD ]
+  default_steps = configure build
+  make_options = -j16
+  build_type = Release
+  packaging_thirdparty = OFF
+  clean_config = ON
+  clean_build = ON
+  test_ref_data_dir = $CASA_TESTS/ref
+  test_run_data_dir = $CASA_TESTS/test
+  brainvisa brainvisa-cmake $CASA_BRANCH $CASA_SRC
+  brainvisa soma-base $CASA_BRANCH $CASA_SRC
+  brainvisa soma-io $CASA_BRANCH $CASA_SRC
+  brainvisa aims-free $CASA_BRANCH $CASA_SRC
+EOF
+
+casa_distro \
+    -r "$CASA_DISTRO_DIR" \
+    bv_maker \
+    distro=aims \
+    branch=bug_fix \
+    system=ubuntu-16.04
+
+casa_distro \
+    -r "$CASA_DISTRO_DIR" \
+    run \
+    distro=aims \
+    branch=bug_fix \
+    system=ubuntu-16.04 \
+    /bin/sh -c 'cd /casa/build && make install-runtime BRAINVISA_INSTALL_PREFIX=/casa/install'
+
+cp -a "$CASA_DISTRO_DIR"/aims/bug_fix_ubuntu-16.04/install .
+
+DOCKER_IMAGE=brainvisa-aims:bug_fix_$(date -Id)
+docker build -t $DOCKER_IMAGE .
+
+docker save -o $DOCKER_IMAGE.tar $DOCKER_IMAGE

docker-backend/Dockerfile

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+FROM brainvisa-aims:latest
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends --no-install-suggests \
+        python3 \
+        python3-pip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install --no-cache-dir -r requirements.txt

hbp_spatial_backend/__init__.py

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+# Copyright 2019 CEA
+# Author: Yann Leprince <[email protected]>
+#
+# This file is part of hbp-spatial-backend.
+#
+# hbp-spatial-backend is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# hbp-spatial-backend is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License
+# for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with hbp-spatial-backend. If not, see <https://www.gnu.org/licenses/>.
+
+import os
+
+import flask
+
+
+# __version__ and SOURCE_URL are used by setup.py and docs/conf.py (they are
+# parsed with a regular expression, so keep the syntax simple).
+__version__ = '0.1.0.dev0'
+
+# URL that holds the source code of the backend. This must be changed to
+# point to the exact code of any modified version, in order to comply with
+# the AGPL licence.
+SOURCE_URL = 'https://github.com/HumanBrainProject/hbp-spatial-backend'
+
+
+class DefaultConfig:
+    CORS_ALLOW_ALL = True
+
+
+# This function has a magic name which is recognized by flask as a factory for
+# the main app.
+def create_app(test_config=None):
+    app = flask.Flask(__name__,
+                      instance_path=os.environ.get("INSTANCE_PATH"),
+                      instance_relative_config=True)
+
+    app.config.from_object(DefaultConfig)
+    if test_config is None:
+        # load the instance config, if it exists, when not testing
+        app.config.from_pyfile("config.py", silent=True)
+        app.config.from_envvar("HBP_SPATIAL_BACKEND_SETTINGS", silent=True)
+    else:
+        # load the test config if passed in
+        app.config.from_mapping(test_config)
+
+    # ensure the instance folder exists
+    try:
+        os.makedirs(app.instance_path)
+    except OSError:
+        pass
+
+    if app.config["CORS_ALLOW_ALL"]:
+        import flask_cors
+        flask_cors.CORS(app)
+
+    @app.route("/source")
+    def root():
+        return flask.redirect(SOURCE_URL)
+
+    import hbp_spatial_backend.api_v1
+    hbp_spatial_backend.api_v1.register_api(app, prefix='/v1')
+
+    return app

hbp_spatial_backend/api_v1.py

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+# Copyright 2019 CEA
+# Author: Yann Leprince <[email protected]>
+#
+# This file is part of hbp-spatial-backend.
+#
+# hbp-spatial-backend is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# hbp-spatial-backend is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License
+# for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with hbp-spatial-backend. If not, see <https://www.gnu.org/licenses/>.
+
+import flask_restful
+import flask_restful.reqparse
+
+
+def tuple_3floats(input_sequence):
+    '''Convert a variable to a tuple of 3 floats
+
+    TypeError is raised if the conversion is not possible.
+    '''
+    input_tuple = tuple(input_sequence)
+    if len(input_tuple) != 3:
+        raise TypeError('the input sequence is not of length 3')
+    return tuple(float(x) for x in input_tuple)
+
+
+class TransformPointApi(flask_restful.Resource):
+    def get(self):
+        parser = flask_restful.reqparse.RequestParser()
+        parser.add_argument('source_space', required=True, location='json')
+        parser.add_argument('target_space', required=True, location='json')
+        parser.add_argument('source_point', required=True,
+                            type=tuple_3floats, location='json')
+        args = parser.parse_args(strict=True)
+        # transform_chain = transform_graph.get_chain(source_space,
+        #                                             target_space)
+        # target_point = apply_transform.transform_point(source_point,
+        #                                                transform_chain)
+        target_point = args.source_point
+        return {'target_point': target_point}
+
+
+def register_api(app, *args, **kwargs):
+    api = flask_restful.Api(app, *args, **kwargs)
+    api.add_resource(TransformPointApi, '/transform-point')

run-flask-dev.sh

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+#! /bin/sh -e
+
+PYTHONPATH=$(dirname -- "$0")${PYTHONPATH+:}$PYTHONPATH
+FLASK_APP=hbp_spatial_backend
+FLASK_ENV=development
+export PYTHONPATH FLASK_APP FLASK_ENV
+
+flask run "$@"

setup.cfg

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+[aliases]
+test = pytest