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Merge pull request #1319 from OpenEnergyPlatform/feature-1020-export-of-existing-terms-and-definitions
Export of existing terms and definitions #1020
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‎.github/workflows/PostReleaseScripts.yml

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name: Post Release Scripts
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# on:
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# workflow_dispatch: {}
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# push:
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# branches:
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# - 'feature-1020-export-of-existing-terms-and-definitions'
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# First we test the setup, to see if the files are building correctly once that is checked we introduce the wiki upload each release.
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on:
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push:
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tags:
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- "v*"
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branches:
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- 'feature-1020-export-of-existing-terms-and-definitions'
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jobs:
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exportTermsDefinitions:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.7'
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architecture: x64
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- uses: actions/setup-java@v2
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with:
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distribution: 'adopt'
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java-version: '11'
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- name: install python dependencies
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run: pip install -r src/scripts/requirements.txt
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- name: setup robot
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run: |
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wget https://github.com/ontodev/robot/releases/download/v1.9.0/robot.jar -O src/robot.jar
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- name: Build ETD xlsx
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run: |
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java -jar src/robot.jar merge --input "src/ontology/oeo.omn" \
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--input "src/ontology/edits/oeo-model.omn" \
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--input "src/ontology/edits/oeo-physical.omn" \
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--input "src/ontology/edits/oeo-shared.omn" \
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--input "src/ontology/edits/oeo-social.omn" \
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--include-annotations true \
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export --header "ID|LABEL|definition" \
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--prefix "OEO: http://openenergy-platform.org/ontology/oeo/OEO_" \
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--sort "LABEL" \
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--export "src/scripts/etd/etd.xlsx"
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- name: Build ETD md
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run: |
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python src/scripts/etd/etd.py
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- name: Upload Artifacts
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uses: actions/upload-artifact@v3
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with:
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name: existing-terms-and-definitions
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path: src/scripts/etd/glossary
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# - name: Checkout wiki
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# uses: actions/checkout@v2
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# with:
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# repository: ${{github.repository}}.wiki
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# path: wiki
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# - name: Push list to wiki
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# run: |
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# cd wiki
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# cp -a ../src/scripts/etd/glossary/. .
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# git config --local user.email "[email protected]"
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# git config --local user.name "GitHub Action"
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# git add .
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# git diff-index --quiet HEAD || git commit -m "Add changes" && git push

‎src/ontology/edits/oeo-physical.omn

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OEO_00010032
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Class: <http://opennergy-plattform.org/ontology/oeo/OEO_00290002>
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Class: <http://openenergy-platform.org/ontology/oeo/oeo-physical/OEO_00290002>
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Annotations:
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<http://purl.obolibrary.org/obo/IAO_0000115> "A surface azimuth angle is a quantity value with a plane angle unit that measures the deviation of the projection on a horizontal plane of the normal to the plane from the local meridian, with zero due south, east negative, and west positive."@en,

‎src/scripts/etd/README.md

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This script generates a glossary for existing terms and definitions formatted in a table in a markdown file.
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The markdown file will be created in the same path (/ontology/src/scripts/etd/).
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Guide:
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1. Make sure you installed python3 and the python module pandas
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2. Call the bash script etd.sh in the directory: ontology/src/scripts/etd

‎src/scripts/etd/etd.py

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import os
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import pandas as pd
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import warnings
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import re
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import string
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import pathlib
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warnings.filterwarnings("ignore")
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import sys
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GLOSSARY_HEADER = """# Existing Terms and Definitions
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"""
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BASE_LINK_WIKI = "https://github.com/OpenEnergyPlatform/ontology/wiki/"
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BASE_IRI = "http://openenergy-platform.org/ontology/oeo/"
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if __name__ == '__main__':
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arguments = sys.argv[1:]
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if len(arguments) > 0:
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target_path = arguments[0]
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else:
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target_path = 'src/scripts/etd'
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cwd = os.getcwd()
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df = pd.read_excel(pathlib.Path(target_path).joinpath("etd.xlsx").as_posix())
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df = df.replace('\n', '<br>', regex=True)
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df = df.sort_values("LABEL", key=lambda col: col.str.strip().str.lower())
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# Create one table per letter:
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pathlib.Path(cwd + "/src/scripts/etd/glossary/").mkdir(parents=True, exist_ok=True)
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# header = GLOSSARY_HEADER + " ".join([f"[{letter}]({BASE_LINK_WIKI}{letter})" for letter in string.ascii_uppercase]) + "\n"
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# with open(cwd + "/src/scripts/etd/glossary/glossary.md", "w") as fil:
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# fil.write(header)
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output = GLOSSARY_HEADER + "\n"
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for letter in string.ascii_lowercase:
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current_df = df[df["LABEL"].str.lower().str.startswith(letter)]
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if current_df.empty:
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continue
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buffer = current_df.to_markdown(index=False)
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buffer = re.sub(r"(?s)(http:\/\/openenergy-platform.org\/ontology\/oeo\/?)\w+-\w+\/(\w+)(?=_)_(\d+?)(?=\s)", r"\2:\3", buffer)
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# There is a weird typo in surface azimuth angle ?
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buffer = re.sub(r"(?s)(http:\/\/opennergy-plattform.org\/ontology\/oeo\/?)\/(\w+)(?=_)_(\d+?)(?=\s)", r"\2:\3", buffer)
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# Remove the thing above when the typo is fixed
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buffer =re.sub(r"(?s)(\w+?)(?=:):(\d+?)(?=\s)", r"[\1:\2]({}".format(BASE_IRI)+ r"\1_\2)", buffer)
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title = f"## {letter.capitalize()}\n\n"
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table = title + buffer + "\n\n"
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#df.to_markdown(buf=cwd + "/src/scripts/etd/ETD.md", index=False)
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output += table
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with open(pathlib.Path(target_path).joinpath("glossary/glossary.md").as_posix(), "w") as fil:
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fil.write(output)
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# create csv output
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df_csv = df.copy()
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df_csv["ID"] = df_csv["ID"].str.replace("http://openenergy-platform.org/ontology/oeo/oeo-physical/", "")
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df_csv["ID"] = df_csv["ID"].str.replace("http://openenergy-platform.org/ontology/oeo/oeo-model/", "")
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df_csv["ID"] = df_csv["ID"].str.replace(":", "_")
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df_csv.to_csv(pathlib.Path(target_path).joinpath("glossary/glossary.csv").as_posix(), index=False)

‎src/scripts/etd/etd.sh

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#!/bin/bash
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if [ -e ETD.md ]
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then
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rm ETD.md
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fi
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SCRIPT_PATH="$PWD"
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ONTO_PATH="$(dirname "$(dirname "$SCRIPT_PATH")")""/ontology/"
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robot merge --input "$ONTO_PATH""oeo.omn" \
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--input "$ONTO_PATH""edits/oeo-model.omn" \
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--input "$ONTO_PATH""edits/oeo-physical.omn" \
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--input "$ONTO_PATH""edits/oeo-shared.omn" \
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--input "$ONTO_PATH""edits/oeo-social.omn" \
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--include-annotations true \
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export --header "LABEL|ID|definition" \
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--prefix "OEO: http://openenergy-platform.org/ontology/oeo/OEO_" \
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--sort "LABEL" \
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--export "$ETD_PATH""etd.xlsx"
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python3 etd.py
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rm etd.xlsx

‎src/scripts/requirements.txt

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pandas
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tabulate
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openpyxl

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