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Merge pull request #297 from tdwg/0.6
Camtrap DP 0.6
2 parents a9c78b3 + 7fd0136 commit 4e5fb0b

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‎_config.yml

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@@ -18,11 +18,22 @@ logo: /assets/theme/images/tdwg-logo-short.svg
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markdown: kramdown
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plugins:
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- jekyll-feed
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- jekyll-sitemap
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exclude:
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- README.md
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- Gemfile
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- Gemfile.lock
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- LICENSE
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- example
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- tests
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- example/*
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- tests/*
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- "*.json"
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# FRONTMATTER DEFAULTS
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defaults:
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- scope:
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path: pages/example
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values:
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permalink: "/example/:basename/"
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layout: example
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title: Example dataset
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toc: true

‎_data/_tables.yml

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- deployments-table-schema
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- media-table-schema
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- observations-table-schema
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- media-observations-table-schema
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- event-observations-table-schema

‎_data/deployments.csv

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../example/deployments.csv

‎_data/event-observations-table-schema.json

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../event-observations-table-schema.json

‎_data/event-observations.csv

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../example/event-observations.csv

‎_data/media-observations-table-schema.json

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../media-observations-table-schema.json

‎_data/media-observations.csv

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../example/media-observations.csv

‎_data/media.csv

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../example/media.csv

‎_data/navigation.yml

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href: /metadata/
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- text: Data
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href: /data/
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- text: Example dataset
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menu:
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- text: Deployment 1
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href: /example/00a2c20d-f038-490c-9b3f-7e32abfa0be7/
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- text: Deployment 2
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href: /example/29b7d356-4bb4-4ec4-b792-2af5cc32efa8/
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- text: Deployment 3
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href: /example/577b543a-2cf1-4b23-b6d2-cda7e2eac372/
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- text: Deployment 4
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href: /example/62c200a9-0e03-4495-bcd8-032944f6f5a1/
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- text: GitHub
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href: https://github.com/tdwg/camtrap-dp

‎_data/observations-table-schema.json

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This file was deleted.

‎_layouts/example.html

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---
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layout: default
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---
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{{ content }}
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<p class="small">Source: <a href="{{ site.github.repository_url }}/blob/main/example"><code>example dataset</code></a></p>
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{% assign dep_id = page.name | remove: '.md' %}
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{% assign dep = site.data.deployments | where: 'deploymentID', dep_id | first %}
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{% assign media = site.data.media | where: 'deploymentID', dep_id %}
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{% assign media_observations = site.data.media-observations %}
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{% assign event_observations = site.data.event-observations %}
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<h2 id="{{ dep_id }}">Deployment information</h2>
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<dl>
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<dt>Location</dt>
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<dd>
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<code>{{ dep.locationName }}</code>
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(<a href="https://www.google.com/maps/search/?api=1&query={{ dep.latitude }},{{ dep.longitude }}&zoom=12"><code>{{ dep.latitude }}, {{ dep.longitude }}</code></a>),
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uncertainty: <code>{{ dep.coordinateUncertainty }}</code>m
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<dd>
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<dt>Duration</dt>
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<dd>
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<code>{{ dep.start }}</code> / <code>{{ dep.end }}</code>
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</dd>
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<dt>Camera setup</dt>
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<dd>
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interval: <code>{{ dep.cameraInterval }}</code>,
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height: <code>{{ dep.cameraHeight }}</code>,
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tilt: <code>{{ dep.cameraTilt }}</code>,
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heading: <code>{{ dep.cameraHeading }}</code>
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</dd>
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<dt>Bait</dt>
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<dd>
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<code>{{ dep.baitUse }}</code>
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</dd>
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</dl>
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{% assign event_ids = media | map: 'eventID' | uniq %}
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{% for event_id in event_ids %}
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{% assign event_media = media | where: 'eventID', event_id %}
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{% assign event_media_count = event_media | size %}
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<h2 id="{{ event_id }}">Event: {{ event_id }}</h2>
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<div id="carousel-{{ event_id }}" class="carousel slide carousel-fade" data-bs-ride="carousel" data-bs-keyboard="false" data-bs-interval="500">
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<div class="carousel-inner">
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{% for med in event_media %}
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{% assign public = med.filePublic | downcase %}
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{% if public == "false" %}
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{% assign public = false %}
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{% else %}
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{% assign public = true %}
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{% endif %}
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<div class="carousel-item{% if forloop.first %} active{% endif %}">
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<img class="d-block w-100" src="{% if public %}{{ med.filePath }}{% else %}{{ '/assets/placeholder.svg' | relative_url }}{% endif %}" alt="{{ med.timestamp }}">
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<div class="carousel-caption d-none d-md-block">
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<p class="fs-1">{{ forloop.index }}</p>
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</div>
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</div>
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{% endfor %}
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</div>
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<button class="carousel-control-prev" type="button" data-bs-target="#carousel-{{ event_id }}" data-bs-slide="prev">
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<span class="carousel-control-prev-icon" aria-hidden="true"></span>
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<span class="visually-hidden">Previous</span>
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</button>
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<button class="carousel-control-next" type="button" data-bs-target="#carousel-{{ event_id }}" data-bs-slide="next">
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<span class="carousel-control-next-icon" aria-hidden="true"></span>
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<span class="visually-hidden">Next</span>
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</button>
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</div>
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<table class="table table-sm mt-4">
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<colgroup>
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<col width="6%">
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<col width="47%">
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<col width="47%">
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</colgroup>
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<thead>
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<tr>
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<th>File</th>
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<th>Media observations</th>
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<th>Event observations</th>
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</tr>
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</thead>
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<tbody>
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{% for med in event_media %}
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{% assign med_id = med.mediaID %}
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<tr>
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<td>
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{{ forloop.index }}
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</td>
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<td title="mediaID: {{ med_id }}">
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{% assign media_obs = media_observations | where: 'mediaID', med_id %}
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{% for obs in media_obs %}
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<code>{{ obs.observationType }}</code>
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{% if obs.observationType == 'animal' %}
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<span class="badge rounded-pill bg-secondary">{{ obs.count }}</span>
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<em>{{ obs.scientificName }}</em>
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{% if obs.lifeStage and obs.sex %}
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({{ obs.lifeStage }}, {{ obs.sex }})
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{% elsif obs.lifeStage %}
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({{ obs.lifeStage }})
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{% elsif obs.sex %}
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({{ obs.sex }})
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{% endif %}
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{% endif %}
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{% if obs.classificationMethod == 'machine' %}
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<span class="text-muted small">Classified by machine</span>
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{% endif %}
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<br>
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{% endfor %}
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</td>
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{% if forloop.first %}
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<td title="eventID: {{ event_id }}" rowspan="{{ event_media_count }}">
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{% assign event_obs = event_observations | where: 'eventID', event_id %}
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{% for obs in event_obs %}
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<code>{{ obs.observationType }}</code>
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{% if obs.observationType == 'animal' %}
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<span class="badge rounded-pill bg-secondary">{{ obs.count }}</span>
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<em>{{ obs.scientificName }}</em>
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{% if obs.lifeStage and obs.sex %}
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({{ obs.lifeStage }}, {{ obs.sex }})
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{% elsif obs.lifeStage %}
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({{ obs.lifeStage }})
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{% elsif obs.sex %}
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({{ obs.sex }})
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{% endif %}
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{% endif %}
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{% if obs.classificationMethod == 'machine' %}
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<span class="text-muted small">Classified by machine</span>
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{% endif %}
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<br>
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{% endfor %}
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</td>
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{% endif %}
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</tr>
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{% endfor %}
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</tbody>
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</table>
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{% endfor %}

‎_layouts/profile.html

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{% assign properties1 = site.data[profile_file].allOf[1].properties %}
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{% assign required1 = site.data[profile_file].allOf[1].required %}
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<p class="small">Source: <a href="https://github.com/{{ site.github_username }}/blob/main/{{ profile_file }}.json"><code>{{ profile_file }}.json</code></a></p>
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<p class="small">Source: <a href="{{ site.github.repository_url }}/blob/main/{{ profile_file }}.json"><code>{{ profile_file }}.json</code></a></p>
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{% for p1_raw in properties1 %}
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{% assign p1_name = p1_raw[0] %}
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{% if p1['skos:exactMatch'] %}
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<p class="small text-muted">Same as <a href="{{ p1['skos:exactMatch'] }}">{{ p1['skos:exactMatch'] }}</a></p>
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{% elsif p1['skos:narrowMatch'] %}
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<p class="small text-muted">Narrower than <a href="{{ p1['skos:narrowMatch'] }}">{{ p1['skos:narrowMatch'] }}</a></p>
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<p class="small text-muted">Broader than <a href="{{ p1['skos:narrowMatch'] }}">{{ p1['skos:narrowMatch'] }}</a></p>
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{% elsif p1['skos:broadMatch'] %}
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<p class="small text-muted">Broader than <a href="{{ p1['skos:broadMatch'] }}">{{ p1['skos:broadMatch'] }}</a></p>
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<p class="small text-muted">Narrower than <a href="{{ p1['skos:broadMatch'] }}">{{ p1['skos:broadMatch'] }}</a></p>
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{% endif %}
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{% if p1.properties %}
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{% elsif p1.items.properties %}
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{% assign properties2 = p1.items.properties %}
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{% assign required2 = p1.items.required %}
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{% elsif p1.items.oneOf[0].properties %}
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{% assign properties2 = p1.items.oneOf[0].properties %}
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{% assign required2 = p1.items.oneOf[0].required %}
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{% else %}
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{% assign properties2 = false %}
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{% endif %}
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{% if p2['skos:exactMatch'] %}
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<span class="small text-muted">Same as <a href="{{ p2['skos:exactMatch'] }}">{{ p2['skos:exactMatch'] }}</a></span>
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{% elsif p2['skos:narrowMatch'] %}
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<span class="small text-muted">Narrower than <a href="{{ p2['skos:narrowMatch'] }}">{{ p2['skos:narrowMatch'] }}</a></span>
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<span class="small text-muted">Broader than <a href="{{ p2['skos:narrowMatch'] }}">{{ p2['skos:narrowMatch'] }}</a></span>
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{% elsif p2['skos:broadMatch'] %}
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<span class="small text-muted">Broader than <a href="{{ p2['skos:broadMatch'] }}">{{ p2['skos:broadMatch'] }}</a></span>
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<span class="small text-muted">Narrower than <a href="{{ p2['skos:broadMatch'] }}">{{ p2['skos:broadMatch'] }}</a></span>
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{% endif %}
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</td>
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<td>{{ p2.type }}</td>
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<td><span class="badge bg-secondary">{{ p2.type }}</span></td>
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</tr>
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{% endfor %}
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</tbody>

‎_layouts/tables.html

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{% for table_schema_file in site.data["_tables"] %}
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{% assign table_schema = site.data[table_schema_file] %}
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{% assign table_schema_id = table_schema.title | downcase | url_encode %}
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{% assign table_schema_id = table_schema.title | downcase | replace: ' ', '-' %}
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<h2 id="{{ table_schema_id }}">{{ table_schema.title }}</h2>
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<p class="small">Source: <a href="https://github.com/{{ site.github_username }}/blob/main/{{ table_schema_file }}.json"><code>{{ table_schema_file }}.json</code></a></p>
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<p class="small">Source: <a href="{{ site.github.repository_url }}/blob/main/{{ table_schema_file }}.json"><code>{{ table_schema_file }}.json</code></a></p>
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{{ table_schema.description | markdownify }}
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<tbody>
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{% for field in table_schema.fields %}
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<tr class="text-break">
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<td id="{{ table_schema_id }}.{{ field.name | downcase | url_encode }}">
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<a href="#{{ table_schema_id }}.{{ field.name | downcase | url_encode }}"><code>{{ field.name }}</code></a>
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<td id="{{ table_schema_id }}.{{ field.name }}">
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<a href="#{{ table_schema_id }}.{{ field.name }}"><code>{{ field.name }}</code></a>
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{% if field.constraints.required %}*{% endif %}
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</td>
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<td>
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{% if field['skos:exactMatch'] %}
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<span class="small text-muted">Same as <a href="{{ field['skos:exactMatch'] }}">{{ field['skos:exactMatch'] }}</a></span>
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{% elsif field['skos:narrowMatch'] %}
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<span class="small text-muted">Narrower than <a href="{{ field['skos:narrowMatch'] }}">{{ field['skos:narrowMatch'] }}</a></span>
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<span class="small text-muted">Broader than <a href="{{ field['skos:narrowMatch'] }}">{{ field['skos:narrowMatch'] }}</a></span>
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{% elsif field['skos:broadMatch'] %}
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<span class="small text-muted">Broader than <a href="{{ field['skos:broadMatch'] }}">{{ field['skos:broadMatch'] }}</a></span>
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<span class="small text-muted">Narrower than <a href="{{ field['skos:broadMatch'] }}">{{ field['skos:broadMatch'] }}</a></span>
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{% endif %}
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</td>
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<td>{{ field.type }}</td>
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<td><span class="badge bg-secondary">{{ field.type }}</span></td>
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</tr>
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{% endfor %}
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</tbody>

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