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update directory structure
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updates the directory structure to includes support for modules/
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@jsimonclark
jsimonclark committed Sep 15, 2024
1 parent 53684ad commit 31cb0bc
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Showing 8 changed files with 183 additions and 80 deletions.
38 changes: 27 additions & 11 deletions .github/workflows/ci_tests.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: CI - Tests
name: EMMO check

on: [pull_request]

Expand All @@ -24,16 +24,32 @@ jobs:
- name: Run EMMO Check - battery
run: |
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
battery.ttl
if [ -f "battery.ttl" ]; then
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
battery.ttl
else
echo "battery.ttl not found!"
exit 1
fi
- name: Run EMMO Check - batteryquantities
run: |
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
batteryquantities.ttl
if [ -f "batteryquantities.ttl" ]; then
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
batteryquantities.ttl
elif [ -f "modules/quantities.ttl" ]; then
emmocheck --verbose --url-from-catalog \
--skip test_namespace \
--skip test_quantity_dimension \
--configfile=.github/utils/emmocheck_config.yml \
modules/quantities.ttl
else
echo "batteryquantities.ttl or modules/quantities.ttl not found!"
exit 1
fi
80 changes: 49 additions & 31 deletions .github/workflows/doc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,10 @@ on:
push:
branches:
- 'master'

pull_request:
branches:
- '*' # To ensure it runs on all PRs

env:
GIT_USER_NAME: BattINFO Developers
GIT_USER_EMAIL: "BattINFO@big-map.org"
Expand All @@ -23,14 +26,14 @@ jobs:
uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v4 #Uses python install action from here: https://github.com/marketplace?type=actions
uses: actions/setup-python@v4
with:
python-version: '3.10' # Replace with the desired Python version
python-version: '3.10'

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install Markdown==3.4.3 rdflib==6.3.2 # Add any other dependencies if needed
pip install Markdown==3.4.3 rdflib==6.3.2 pandoc
- name: Render documentation from ttl
run: python docs/scripts/ttl_to_rst.py
Expand All @@ -40,25 +43,24 @@ jobs:
with:
docs-folder: "docs/"
pre-build-command: "apt-get update -y; apt-get install -y pandoc"

- name: Create context file from ttl
run: python docs/scripts/ttl_to_context.py

- name: Check if HTML context directory exists
run: |
if [ ! -d "docs/_build/html/context/" ]; then
echo "Creating HTML context directory"
sudo mkdir -p docs/_build/html/context/
else
echo "HTML context directory already exists"
fi
if [ ! -d "docs/_build/html/assets/" ]; then
sudo mkdir -p docs/_build/html/assets/
fi
if [ ! -d "docs/_build/html/versions/" ]; then
echo "Creating HTML versions directory"
sudo mkdir -p docs/_build/html/versions/
else
echo "HTML versions directory already exists"
fi
- name: Copy assets directory to HTML directory
run: sudo cp -r docs/assets/* docs/_build/html/assets/

- name: Copy context file to HTML directory
run: sudo cp context/context.json docs/_build/html/context/
Expand All @@ -68,53 +70,69 @@ jobs:
git config --local user.email "${{ env.GIT_USER_EMAIL }}"
git config --local user.name "${{ env.GIT_USER_NAME }}"
git add context/context.json
# Check for any changes to commit
git diff --staged --quiet || git commit -m "Update context.json file"
- name: Pull latest changes
if: github.event_name == 'push' # Only pull changes during push events
run: git pull origin master --rebase

- name: Push changes
if: github.event_name == 'push' && github.ref == 'refs/heads/master' # Only push during push events on master
run: git push origin HEAD:master

- name: Fetch all tags and create version directories
run: |
git fetch --tags
git tag | while read TAG; do
sudo mkdir -p "docs/_build/html/versions/$TAG"
if [ -f "batteryquantities.ttl" ]; then
python docs/scripts/apply_foops_recommendations.py batteryquantities.ttl batteryquantities-foops.ttl
sudo cp "batteryquantities-foops.ttl" "docs/_build/html/versions/$TAG/batteryquantities.ttl"
elif [ -f "modules/quantities.ttl" ]; then
python docs/scripts/apply_foops_recommendations.py modules/quantities.ttl quantities-foops.ttl
sudo cp "quantities-foops.ttl" "docs/_build/html/versions/$TAG/quantities.ttl"
else
echo "File not found!"
exit 1
fi
python docs/scripts/apply_foops_recommendations.py battery.ttl battery-foops.ttl
python docs/scripts/apply_foops_recommendations.py batteryquantities.ttl batteryquantities-foops.ttl
sudo cp "battery-foops.ttl" "docs/_build/html/versions/$TAG/"
sudo cp "batteryquantities-foops.ttl" "docs/_build/html/versions/$TAG/"
sudo cp "battery-foops.ttl" "docs/_build/html/versions/$TAG/battery.ttl"
sudo cp "battery-inferred.ttl" "docs/_build/html/versions/$TAG/"
if [ -d "context" ]; then
echo "Context directory exists, copying context.json to $TAG"
# Make sure the context directory exists in the version-specific directory
sudo mkdir -p "docs/_build/html/versions/$TAG/context"
# Copy context.json to the tag-specific context directory
sudo cp "context/context.json" "docs/_build/html/versions/$TAG/context"
else
echo "No context directory found in the source directory."
fi
if [ -d "context" ]; then
sudo mkdir -p "docs/_build/html/versions/$TAG/context"
sudo cp "context/context.json" "docs/_build/html/versions/$TAG/context"
fi
done
- name: Copy TTL files to HTML directory
run: |
if [ -f "batteryquantities.ttl" ]; then
python docs/scripts/apply_foops_recommendations.py batteryquantities.ttl batteryquantities-foops.ttl
sudo cp "batteryquantities-foops.ttl" "docs/_build/html/batteryquantities.ttl"
elif [ -f "modules/quantities.ttl" ]; then
python docs/scripts/apply_foops_recommendations.py modules/quantities.ttl quantities-foops.ttl
sudo cp "quantities-foops.ttl" "docs/_build/html/quantities.ttl"
else
echo "battery quantities file not found!"
exit 1
fi
python docs/scripts/apply_foops_recommendations.py battery.ttl battery-foops.ttl
python docs/scripts/apply_foops_recommendations.py batteryquantities.ttl batteryquantities-foops.ttl
sudo cp "battery-foops.ttl" "docs/_build/html/battery.ttl"
sudo cp "batteryquantities-foops.ttl" "docs/_build/html/batteryquantities.ttl"
sudo cp "battery-inferred.ttl" "docs/_build/html/battery-inferred.ttl"

- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: documentationHTML
path: docs/_build/html/

- name: Deploy
if: github.ref == 'refs/heads/master' && github.event_name == 'push' # Only deploy during push events on master
uses: peaceiris/actions-gh-pages@v3
if: github.ref == 'refs/heads/master'
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: docs/_build/html


16 changes: 8 additions & 8 deletions battery.ttl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,9 @@
@base <https://w3id.org/emmo/domain/battery/battery> .

<https://w3id.org/emmo/domain/battery/battery> rdf:type owl:Ontology ;
owl:versionIRI <https://w3id.org/emmo/domain/battery/0.12.1-beta/battery> ;
owl:imports <https://w3id.org/emmo/domain/battery/0.12.1-beta/batteryquantities> ,
<https://w3id.org/emmo/domain/electrochemistry/0.20.0-beta/electrochemistry> ;
owl:versionIRI <https://w3id.org/emmo/domain/battery/0.13.0-beta/battery> ;
owl:imports <https://w3id.org/emmo/domain/battery/0.13.0-beta/modules/quantities> ,
<https://w3id.org/emmo/domain/electrochemistry/0.22.0-beta/electrochemistry> ;
dcterms:abstract "The Battery Domain Ontology, a specialized domain within the Elementary Multiperspective Materials Ontology (EMMO), encompasses essential terms and relationships for battery components, cells, interfaces, methods, models, and data. Its primary objective is to enable the creation of linked and FAIR (Findable, Accessible, Interoperable, and Reusable) data, thereby fostering advancements in research and innovation within the realm of batteries. This ontology serves as a foundational resource for harmonizing battery knowledge representation, enhancing data interoperability, and accelerating progress in battery research and development." ;
dcterms:bibliographicCitation "https://zenodo.org/doi/10.5281/zenodo.7693672" ;
dcterms:contributor <https://orcid.org/0000-0001-8869-3718> ,
Expand All @@ -28,19 +28,19 @@
dcterms:created "2022-11-25"^^xsd:date ;
dcterms:creator <https://orcid.org/0000-0002-8758-6109> ,
<https://orcid.org/0000-0003-2954-1233> ;
dcterms:issued "2024-07-24"^^xsd:date ;
dcterms:issued "2024-09-15"^^xsd:date ;
dcterms:license "https://creativecommons.org/licenses/by/4.0/legalcode" ;
dcterms:modified "2024-07-24"^^xsd:date ;
dcterms:modified "2024-09-15"^^xsd:date ;
dcterms:publisher "EMMO" ;
dcterms:source <https://www.electropedia.org> ;
dcterms:title "Battery Domain Ontology"@en ;
bibo:doi "10.5281/zenodo.7693672" ;
bibo:status "unstable" ;
vann:preferredNamespacePrefix "battery" ;
vann:preferredNamespaceUri "https://w3id.org/emmo/domain/battery" ;
owl:backwardCompatibleWith "0.12.0-beta" ;
owl:priorVersion "0.12.0-beta" ;
owl:versionInfo "0.12.1-beta" ;
owl:backwardCompatibleWith "0.12.1beta" ;
owl:priorVersion "0.12.1beta" ;
owl:versionInfo "0.13.0-beta" ;
foaf:logo "https://raw.githubusercontent.com/emmo-repo/domain-battery/master/docs/assets/img/fig/png/domain-battery-logo.png" .

#################################################################
Expand Down
12 changes: 6 additions & 6 deletions catalog-v001.xml
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="Imports Wizard Entry" name="https://w3id.org/emmo/domain/electrochemistry/0.20.0-beta/electrochemistry" uri="https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/0.20.0-beta/electrochemistry.ttl"/>
<uri id="Imports Wizard Entry" name="https://w3id.org/emmo/domain/electrochemistry/0.20.0-beta/electrochemicalquantities" uri="https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/0.20.0-beta/electrochemicalquantities.ttl"/>
<uri id="Imports Wizard Entry" name="https://w3id.org/emmo/domain/electrochemistry/0.22.0-beta/electrochemistry" uri="https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/0.22.0-beta/electrochemistry.ttl"/>
<uri id="Imports Wizard Entry" name="https://w3id.org/emmo/domain/electrochemistry/0.22.0-beta/modules/quantities" uri="https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/0.22.0-beta/modules/quantities.ttl"/>
<uri id="Imports Wizard Entry" name="https://w3id.org/emmo/1.0.0-beta7" uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta7/emmo.ttl"/>
<group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
<uri name="https://w3id.org/emmo/domain/battery/0.12.1-beta/battery" uri="./battery.ttl"/>
<uri name="https://w3id.org/emmo/domain/battery/0.12.1-beta/batteryquantities" uri="./batteryquantities.ttl"/>
<uri name="https://w3id.org/emmo/domain/battery/0.1.0-beta/battery-products" uri="./battery-products.ttl"/>
<uri name="https://w3id.org/emmo/domain/battery/0.13.0-beta/battery" uri="./battery.ttl"/>
<uri name="https://w3id.org/emmo/domain/battery/0.13.0-beta/modules/quantities" uri="./modules/quantities.ttl"/>
<uri name="https://w3id.org/emmo/domain/battery/0.13.0-beta/products" uri="./modules/products.ttl"/>

<uri name="https://w3id.org/emmo/domain/chemical-substance/0.7.0-beta/chemical-substance" uri="https://raw.githubusercontent.com/emmo-repo/domain-chemical-substance/main/chemical-substance.ttl"/>
<uri name="https://w3id.org/emmo/domain/chemical-substance/0.8.0-beta/chemical-substance" uri="https://raw.githubusercontent.com/emmo-repo/domain-chemical-substance/main/chemical-substance.ttl"/>
<uri name="https://w3id.org/emmo/domain/characterisation-methodology/chameo" uri="https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/main/chameo.ttl"/>

<uri name="https://w3id.org/emmo/1.0.0-beta7/mereocausality" uri="https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta7/mereocausality/mereocausality.ttl"/>
Expand Down
50 changes: 29 additions & 21 deletions docs/scripts/ttl_to_rst.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
from rdflib import Graph
import os



Expand Down Expand Up @@ -83,6 +84,10 @@ def entities_to_rst(entities: list[dict]) -> str:
rst = ""

for item in entities:
# Check if '#' is in the IRI
if '#' not in item['IRI']:
print(f"Skipping IRI without '#': {item['IRI']}")
continue # Skip this entity if no hash is present

iri_prefix, iri_suffix = item['IRI'].split("#")

Expand All @@ -95,7 +100,7 @@ def entities_to_rst(entities: list[dict]) -> str:
rst += "\n\n"

rst += "* " + item['IRI'] + "\n\n"

rst += ".. raw:: html\n\n"
indent = " "
rst += indent + "<table class=\"element-table\">\n"
Expand All @@ -107,12 +112,13 @@ def entities_to_rst(entities: list[dict]) -> str:
rst += indent + "<td class=\"element-table-key\"><span class=\"element-table-key\">" + key + "</span></td>\n"
if value.startswith("http"):
value = f"""<a href='{value}'>{value}</a>"""
value = value.encode('ascii', 'xmlcharrefreplace')
value = value.decode('utf-8')
value = value.replace('\n', '\n' + indent)
else:
value = value.encode('ascii', 'xmlcharrefreplace')
value = value.decode('utf-8')
value = value.replace('\n', '\n' + indent)
rst += indent + "<td class=\"element-table-value\">" + value + "</td>\n"
rst += indent + "</tr>\n"

rst += indent + "</table>\n"
rst += "\n\n"

Expand All @@ -130,38 +136,40 @@ def render_rst_bottom() -> str:

########### RUN THE RENDERING WORKFLOW ##############


def rendering_workflow():

# PAGES
ttl_modules = [
{"section title": "Battery Concepts",
"path": "./battery.ttl"},
{"section title": "Battery Quantities",
"path": "./batteryquantities.ttl"}
]
# Adapt based on file structure
ttl_modules = []

# Check for old structure (root directory)
if os.path.isfile("./batteryquantities.ttl"):
ttl_modules.append({"section title": "Quantities used in Batteries", "path": "./batteryquantities.ttl"})
elif os.path.isfile("./modules/quantities.ttl"):
ttl_modules.append({"section title": "Quantities used in Batteries", "path": "./modules/quantities.ttl"})
else:
raise FileNotFoundError("No suitable TTL file found for battery quantities.")

# Check for the battery file in the correct directory
if os.path.isfile("./battery.ttl"):
ttl_modules.append({"section title": "Battery Concepts", "path": "./battery.ttl"})
else:
raise FileNotFoundError("No suitable TTL file found for battery concepts.")

# GENERATE PAGES
rst_filename = "battery.rst"

rst = render_rst_top()

for module in ttl_modules:

g = load_ttl_from_url(module["path"])

entities_list = extract_terms_info_sparql(g)

page_title = module["section title"]
rst += page_title + "\n"
for ind in range(len(page_title)):
rst += "="
rst += "\n\n"
rst += "=" * len(page_title) + "\n\n"
rst += entities_to_rst(entities_list)

rst += render_rst_bottom()

with open("./docs/"+ rst_filename, "w+", encoding="utf-8") as f:
with open("./docs/" + rst_filename, "w+", encoding="utf-8") as f:
f.write(rst)


Expand Down
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