Merge pull request #107 from DataONEorg/develop

Add gh-pages website for repo, MOSAiC 1.0.1, and various MOSAiC extras
DataONEorg · Sep 14, 2021 · f3f39ff · f3f39ff
2 parents 26c45df + baf43bd
commit f3f39ff
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diff --git a/.github/ontologies.txt b/.github/ontologies.txt
@@ -0,0 +1 @@
+MOSAiC,The MOSAiC Ontology,./MOSAiC/MOSAiC.owl
diff --git a/.github/validate.sh b/.github/validate.sh
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+set -e
+
+RIOT="./apache-jena-4.1.0/bin/riot"
+PATHS=$(cat .github/ontologies.txt | awk -F, '{print $3}')
+
+for path in "$PATHS"
+do
+  "$RIOT" --validate $path
+done
diff --git a/.github/website/build.py b/.github/website/build.py
@@ -0,0 +1,113 @@
+import os
+import shutil
+from pathlib import Path
+import xml
+import pylode
+from jinja2 import Template
+
+
+BASEDIR = os.path.dirname(os.path.realpath(__file__))
+ONTOLOGIES_FILE = os.path.join(BASEDIR, "../ontologies.txt")
+INDEX_TEMPLATE = os.path.join(BASEDIR, "index.template")
+
+
+def get_build_dir():
+    return Path(BASEDIR, "_build")
+
+
+def create_build_dir():
+    tmpdir = get_build_dir()
+
+    if not os.path.exists(tmpdir):
+        os.mkdir(tmpdir)
+
+
+def get_ontologies():
+    with open(ONTOLOGIES_FILE) as onto_file:
+        files = [tuple(line.rstrip("\n").split(",")) for line in onto_file.readlines()]
+        return [{"name": file[0], "title": file[1], "path": file[2]} for file in files]
+
+
+def parse_ontology(path):
+    return {"name": path.replace(".html", ""), "path": path}
+
+
+def process_ontology(ontology):
+    path = ontology["path"]
+    print(f"Processing {path}...")
+
+    # Copy owl file to build dir so it's available
+    newpath = Path(get_build_dir(), os.path.basename(path))
+    shutil.copy(path, newpath)
+
+    # Try processing once. If it fails, try processing as Turtle
+    try:
+        return run_pylode(newpath)
+    except Exception:
+        print("Re-processing as Turtle...")
+        renamedpath = os.path.join(
+            get_build_dir(), os.path.basename(newpath).replace(".owl", ".ttl")
+        )
+        os.rename(newpath, renamedpath)
+
+        return run_pylode(renamedpath)
+
+
+def run_pylode(path):
+    out_path = os.path.join(get_build_dir(), f"{path}.html")
+    out_path = out_path.replace(".ttl", "")
+    out_path = out_path.replace(".owl", "")
+
+    print(f"Running PyLODE on {path} with output path of {out_path}")
+    html = pylode.MakeDocco(
+        input_data_file=str(path), outputformat="html", profile="dataone"
+    ).document()
+
+    with open(out_path, "w") as html_file:
+        html_file.write(str(html))
+
+    return out_path
+
+
+def process_ontologies():
+    for ontology in get_ontologies():
+        process_ontology(ontology)
+
+
+def copy_pylode_output():
+    new_paths = []
+
+    for path in get_build_dir().glob("*.html"):
+        print(f"Copying HTML for {path}")
+
+        basename = os.path.basename(path)
+        new_path = Path(BASEDIR, basename)
+        os.rename(path, new_path)
+        new_paths.append(os.path.basename(new_path))
+
+    return new_paths
+
+
+def build_index():
+    print("Building index...")
+    ontologies = get_ontologies()
+
+    output = None
+
+    with open(INDEX_TEMPLATE, "r") as index_template:
+        tmpl_str = index_template.read()
+        tmpl = Template(tmpl_str)
+        output = tmpl.render(ontologies=ontologies)
+
+    with open(os.path.join(get_build_dir(), "index.html"), "w") as index_html:
+        index_html.write(str(output))
+
+
+def main():
+    create_build_dir()
+    process_ontologies()
+    build_index()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/.github/website/index.template b/.github/website/index.template
@@ -0,0 +1,81 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+    <title>sem-prov-ontologies</title>
+    <style>
+      body {
+        font-size: 16px;
+        font-family: "Open Sans", -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
+        max-width: 660px;
+        margin: 0 auto;
+        color: rgb(34, 34, 34);
+        padding: 1em;
+      }
+
+      header h1 {
+        margin: 0;
+        padding: 0;
+      }
+
+      header a {
+        font-variant: small-caps;
+        font-weight: normal;
+        text-decoration: none;
+        color: #14A2A7;
+      }
+
+      a {
+        color: #1EAEDB;
+      }
+
+      footer {
+        font-size: 80%;
+      }
+    </style>
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <meta name="description" content="DataONE Ontologies">
+  </head>
+  <body>
+    <header>
+      <h1>
+        <a href="/">
+          <svg width="245" height="55" viewBox="0 0 490 109" xmlns="http://www.w3.org/2000/svg">
+            <defs>
+              <linearGradient x1="1.12436655%" y1="50%" x2="97.6641681%" y2="50%" id="linearGradient-1">
+                <stop stop-color="#1B435D" offset="0%"></stop>
+                <stop stop-color="#14A2A7" offset="39.916443%"></stop>
+                <stop stop-color="#14A2A7" offset="53.6578157%"></stop>
+                <stop stop-color="#23678F" offset="100%"></stop>
+            </linearGradient>
+            </defs>
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+          Ontologies
+        </a>
+      </h1>
+    </header>
+    <main>
+      <p>
+        <a href="https://www.dataone.org/">DataONE</a> maintains and develops a family of both general-purpose and domain-specific <a href="https://www.w3.org/OWL/">OWL</a> ontologies:
+      </p>
+      <ul>
+        {% for ontology in ontologies %}
+          <li><a href="https://purl.dataone.org/provone-v1-dev">ProvONE</a></li>
+          <li><a href="http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl">OBOE</a> [<a href="https://github.com/NCEAS/oboe/">GitHub</a>]</li>
+          <li><a href="https://purl.dataone.org/odo/ECSO_">ECSO</a></li>
+          <li><a href="./{{ontology.name}}.html">{{ontology.title}}</a> [<a href="{{ontology.name}}.owl">OWL</a>]</li>
+          <li>ARCRC (WIP)</li>
+          <li>SALMO (WIP)</li>
+          <li>SASAP (WIP)</li>
+        {% endfor %}
+      </ul>
+      <p>
+        <svg aria-hidden="true" class="octicon octicon-mark-github" height="18" role="img" version="1.1" viewBox="0 0 16 16" width="18"><path d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59 0.4 0.07 0.55-0.17 0.55-0.38 0-0.19-0.01-0.82-0.01-1.49-2.01 0.37-2.53-0.49-2.69-0.94-0.09-0.23-0.48-0.94-0.82-1.13-0.28-0.15-0.68-0.52-0.01-0.53 0.63-0.01 1.08 0.58 1.23 0.82 0.72 1.21 1.87 0.87 2.33 0.66 0.07-0.52 0.28-0.87 0.51-1.07-1.78-0.2-3.64-0.89-3.64-3.95 0-0.87 0.31-1.59 0.82-2.15-0.08-0.2-0.36-1.02 0.08-2.12 0 0 0.67-0.21 2.2 0.82 0.64-0.18 1.32-0.27 2-0.27 0.68 0 1.36 0.09 2 0.27 1.53-1.04 2.2-0.82 2.2-0.82 0.44 1.1 0.16 1.92 0.08 2.12 0.51 0.56 0.82 1.27 0.82 2.15 0 3.07-1.87 3.75-3.65 3.95 0.29 0.25 0.54 0.73 0.54 1.48 0 1.07-0.01 1.93-0.01 2.2 0 0.21 0.15 0.46 0.55 0.38C13.71 14.53 16 11.53 16 8 16 3.58 12.42 0 8 0z"></path></svg>
+        Learn more or even get involved at our <a href="https://github.com/DataONEorg/sem-prov-ontologies">GitHub repository</a>
+      </p>
+    </main>
+    <footer>
+      DataONE is a collaboration among many partner organizations, and is funded by the US National Science Foundation (NSF) under a Cooperative Agreement. Acknowledgement: This material is based upon work supported by the National Science Foundation under Grant Numbers 0830944 and 1430508. Disclaimer: Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
+    </footer>
+  </body>
+</html>
diff --git a/.github/workflows/check_mosaic.yml b/.github/workflows/check_mosaic.yml
@@ -0,0 +1,27 @@
+name: Check MOSAiC
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+jobs:
+  correspondence:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+      - run: python -m pip install -r ./MOSAiC/dev/check/requirements.txt
+      - run: python ./MOSAiC/dev/check/check.py
+  schacl:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+      - run: python -m pip install pyshacl
+      - run: pyshacl -s ./MOSAiC/dev/shapes.shacl -df xml -sf turtle ./MOSAiC/MOSAiC.owl
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,39 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-java@v2
+        with:
+          distribution: 'adopt'
+          java-version: '11'
+      - run: curl -O https://mirror.nodesdirect.com/apache/jena/binaries/apache-jena-4.1.0.tar.gz
+      - run: tar xzf apache-jena-4.1.0.tar.gz
+      - run: sh ./.github/validate.sh
+
+  website:
+    needs: validate
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+      - run: python -m pip install -r https://raw.githubusercontent.com/amoeba/pyLODE/master/requirements.txt
+      - run: python -m pip install git+https://github.com/amoeba/pylode.git
+      - run: python -m pip install jinja2
+      - run: python ./.github/website/build.py
+      - name: ghpages
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: ./.github/website/_build