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Co-authored-by: isti-xander <[email protected]>

.github/workflows/yasmine.yml

@@ -0,0 +1,80 @@
+name: Yasmine
+on: [ push ]
+jobs:
+  lint_python:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.6.x'
+      - run: pip install pep8
+      - run: pep8 backend/yasmine
+
+  build_app:
+    runs-on: ubuntu-latest
+    container: ghcr.io/iris-edu/yasmine-stationxml-editor/yasmine-utils:latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Add CI_COMMIT_SHORT_SHA env property with commit short sha
+        run: echo "CI_COMMIT_SHORT_SHA=`echo ${GITHUB_SHA} | cut -c1-8`" >> $GITHUB_ENV
+      - name: Get the version
+        id: get_version
+        run: echo ::set-output name=VERSION::$(echo $GITHUB_REF | cut -d / -f 3)
+      - name: Get TIMESTAMP
+        id: date
+        run: echo "::set-output name=date::$(date --utc --rfc-2822)"
+      - name: Build application
+        env:
+          VERSION_FILE: "yasmine/static/js/yasmine/classic/app.js"
+          CI_JOB_TIMESTAMP: "${{ steps.date.outputs.date }}"
+          CI_COMMIT_TAG: "${{ steps.get_version.outputs.VERSION }}"
+        run: |
+          cd frontend
+          sencha app build
+          cd ../backend
+          echo "$(echo var releaseVersion=\"$CI_COMMIT_TAG\" | cat - $VERSION_FILE)" > $VERSION_FILE
+          echo "$(echo var buildTimestamp=\"$CI_JOB_TIMESTAMP\" | cat - $VERSION_FILE)" > $VERSION_FILE
+          echo "$(echo var commitRevision=\"$CI_COMMIT_SHORT_SHA\" | cat - $VERSION_FILE)" > $VERSION_FILE
+          python3.6 setup.py sdist
+      - uses: actions/upload-artifact@v2
+        with:
+          name: yasmine-artifact
+          path: backend/dist/*.gz
+
+  test_app:
+    runs-on: ubuntu-latest
+    container: ghcr.io/iris-edu/yasmine-stationxml-editor/yasmine-utils:latest
+    needs: [build_app]
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: yasmine-artifact
+      - name: Install and Run Yasmine tests
+        run: |
+          sudo pip3.6 install numpy
+          sudo pip3.6 install YASMINE-1.0.tar.gz
+          yasmineapp.py syncdb upgrade heads
+          yasmineapp.py runserver &>/dev/null&
+          sleep 10
+          yasmineapp.py test
+
+
+#  docker:
+#    runs-on: ubuntu-latest
+#    permissions:
+#      contents: read
+#      packages: write
+#    steps:
+#      - name: Check Out Repo
+#        uses: actions/checkout@v2
+#
+#      - name: Log in to registry
+#        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+#
+#      - name: Build image
+#        run: docker build . --file docker-gitlab-centos7 --tag ghcr.io/iris-edu/yasmine-stationxml-editor/yasmine-utils:latest
+#
+#      - name: Push image
+#        run: docker push ghcr.io/iris-edu/yasmine-stationxml-editor/yasmine-utils:latest

.gitignore

@@ -1,129 +1,5 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# 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/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
+.settings
+.vscode/
+.DS_Store
+/.gradle/
+/.idea/

CHANGELOG.txt

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+Yasmine v2.1.0, 2019/12/06
+
+- 1. Extract specific elements from a stationXML file to populate the user libraries
+- 2. Use of a user-defined instrument atomic library
+- 3. Use of user-defined objects libraries (comments, geology, vault, units ....)
+- 11. Environment setup

README.md

@@ -1 +1,26 @@
-# yasmine-stationxml-editor
+# YASMINE
+
+YASMINE (instrumentation metadata construction tool) is a python web application developed to generate metadata XML for a seismic stations.
+
+## Requirements
+
+1. Installed Python 3.6.5+
+2. Related python packages will be installed automatically by pip
+
+## Instructions to install (under super user rights)
+
+1. Install a source distribution package ``pip install YASMINE-x.x.tar.gz``
+2. Update database ``python yasmineapp.py syncdb upgrade heads``
+3. If there is no internet connection unzip NRL (IRIS.zip) in to the application data folder "/opt/YASMINE/_media/" or "c:/YASMINE/_media/nrl/" depending on OS (Linux/Windows based).
+4. Start application ``python yasmineapp.py runserver``
+
+## Instructions to run using Docker
+
+1. Install Docker <https://www.docker.com/products/docker-desktop>
+2. Run `docker-compose up` to download, build and deploy docker container
+3. Open browser and type `http://localhost:1841`
+
+## Instructions to develop
+
+1. To develop frontend, please go to `frontend` folder and see `README.md` file
+2. To develop backend, please go to `backend` folder and see `README.md` file

backend/.gitignore

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+*.pyc
+dist
+*.egg-info
+.settings
+.idea
+geckodriver.log
+build
+/ghostdriver.log
+/.pydevproject
+.vscode/*
+/debug.log
+*ghostdriver.log
+*debug.log
+/yasmine/static/js/yasmine/
+/yasmine/app/tests/integration/out/
+/venv/

backend/Dockerfile

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+# ****************************************************************************
+#
+# This file is part of the yasmine editing tool.
+#
+# yasmine (Yet Another Station Metadata INformation Editor), a tool to
+# create and edit station metadata information in FDSN stationXML format,
+# is a common development of IRIS and RESIF.
+# Development and addition of new features is shared and agreed between * IRIS and RESIF.
+#
+#
+# Version 1.0 of the software was funded by SAGE, a major facility fully
+# funded by the National Science Foundation (EAR-1261681-SAGE),
+# development done by ISTI and led by IRIS Data Services.
+# Version 2.0 of the software was funded by CNRS and development led by * RESIF.
+#
+# This program is free software; you can redistribute it
+# and/or modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version. *
+# This program 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 Lesser General Public License (GNU-LGPL) for more details. *
+# You should have received a copy of the GNU Lesser General Public
+# License along with this software. If not, see
+# <https://www.gnu.org/licenses/>
+#
+#
+# 2019/10/07 : version 2.0.0 initial commit
+#
+# ****************************************************************************/
+
+FROM python:3.6.5-slim
+ADD . /opt/YASMINE/src
+WORKDIR /opt/YASMINE/src
+
+RUN apt-get update && apt-get install -y wget unzip gnupg
+
+RUN wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
+RUN sh -c 'echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list'
+RUN apt-get update
+RUN apt-get -y install google-chrome-stable
+
+RUN cd /tmp && \
+    wget https://chromedriver.storage.googleapis.com/2.39/chromedriver_linux64.zip -O chromedriver.zip --progress=bar:force && \
+    mkdir /opt/chromedriver && unzip -q -p chromedriver.zip > /opt/chromedriver/chromedriver && \
+    ln -s /opt/chromedriver/chromedriver /usr/local/bin/chromedriver && \
+    rm chromedriver.zip && \
+    chmod +x /opt/chromedriver/chromedriver
+
+RUN pip install -r requirements.txt
+CMD python yasmineapp.py syncdb upgrade heads ; python yasmineapp.py runserver --debug
+

backend/MANIFEST.in

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+include README.rst
+include requirements.txt
+recursive-include  yasmine/static *
+recursive-include  yasmine/templates *
+recursive-include  yasmine/resources *
+recursive-include  yasmine/app/tests/integration/data *
+recursive-include  yasmine/app/tests/unit/data *
+recursive-include  yasmine *.ini
+recursive-include  yasmine/alembic *
+recursive-include  yasmine/tests *

backend/README.md

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+# YASMINE Backend
+If GUI is required to be used, please see `../frontend/README.md` before using backend
+
+## For Users
+### Using locally installed Python
+1. Install Python 3.6.5+
+2. Install numpy>=1.6.1
+3. Run `pip install -r requirements.txt` to install dependencies
+4. Run `python yasmineapp.py syncdb upgrade heads` to migrate database
+5. Start application `python yasmineapp.py runserver`
+
+### Using Docker
+1. Install Docker <https://www.docker.com/products/docker-desktop>
+2. Build Docker image: `docker build -t yasmine/backend .`
+3. Run Docker image: `docker run --rm -p 80:80 yasmine/backend`
+4. Go to GUI url: <http://localhost>
+5. Go to REST API endpoint: <http://localhost/api/>
+
+## For Developers
+### Using locally installed Python
+1. Install Python 3.6.5+
+2. Install numpy>=1.6.1   
+3. (optional) Selenium FireFox driver <https://github.com/mozilla/geckodriver/releases> should be added to the system path
+4. Run `pip install -r requirements.txt` to install dependencies
+5. (optional) Run `python yasmineapp.py syncdb revision --autogenerate` to create migration script
+6. Run `python yasmineapp.py syncdb upgrade heads` to migrate database
+7. (optional) Run `python yasmineapp.py test` to run tests
+8. Start application `python yasmineapp.py runserver`
+
+### Using Docker
+1. Install Docker <https://www.docker.com/products/docker-desktop>
+2. Build Docker image: `docker build -t yasmine/backend .`
+3. Run Docker image: `docker run --rm -p 80:80 yasmine/backend`
+4. Go to GUI url: <http://localhost>
+5. Go to REST API endpoint: <http://localhost/api/>