Merge pull request #286 from tdwg/term-updates

Updates before splitting the observation table

_config.yml

@@ -24,6 +24,16 @@ exclude:
   - Gemfile
   - Gemfile.lock
   - LICENSE
-  - example
-  - tests
+  - example/*
+  - tests/*
   - "*.json"
+
+# FRONTMATTER DEFAULTS
+defaults:
+  - scope:
+      path: pages/example
+    values:
+      permalink: "/example/:basename/"
+      layout: example
+      title: Example dataset
+      toc: true

_data/deployments.csv

@@ -0,0 +1 @@
+../example/deployments.csv

_data/media-observations.csv

@@ -0,0 +1 @@
+../example/media-observations.csv

_data/media.csv

@@ -0,0 +1 @@
+../example/media.csv

_data/navigation.yml

@@ -6,5 +6,15 @@
   href: /metadata/
 - text: Data
   href: /data/
+- text: Example dataset
+  menu:
+  - text: Deployment 1
+    href: /example/00a2c20d-f038-490c-9b3f-7e32abfa0be7/
+  - text: Deployment 2
+    href: /example/29b7d356-4bb4-4ec4-b792-2af5cc32efa8/
+  - text: Deployment 3
+    href: /example/577b543a-2cf1-4b23-b6d2-cda7e2eac372/
+  - text: Deployment 4
+    href: /example/62c200a9-0e03-4495-bcd8-032944f6f5a1/
 - text: GitHub
   href: https://github.com/tdwg/camtrap-dp

_data/observations.csv

@@ -0,0 +1 @@
+../example/observations.csv

_layouts/example.html

@@ -0,0 +1,136 @@
+---
+layout: default
+---
+
+{{ content }}
+
+<p class="small">Source: <a href="{{ site.github.repository_url }}/blob/main/example"><code>example dataset</code></a></p>
+
+{% assign dep_id = page.name | remove: '.md' %}
+{% assign dep = site.data.deployments | where: 'deploymentID', dep_id | first %}
+{% assign media = site.data.media | where: 'deploymentID', dep_id %}
+{% assign media_observations = site.data.media-observations %}
+{% assign event_observations = site.data.observations %}
+
+<h2 id="{{ dep_id }}">Deployment information</h2>
+
+<dl>
+  <dt>Location</dt>
+  <dd>
+    <code>{{ dep.locationName }}</code>
+    (<a href="https://www.google.com/maps/search/?api=1&query={{ dep.latitude }},{{ dep.longitude }}&zoom=12"><code>{{ dep.latitude }}, {{ dep.longitude }}</code></a>),
+    uncertainty: <code>{{ dep.coordinateUncertainty }}</code>m
+  <dd>
+  <dt>Duration</dt>
+  <dd>
+    <code>{{ dep.start }}</code> / <code>{{ dep.end }}</code>
+  </dd>
+  <dt>Camera setup</dt>
+  <dd>
+    interval: <code>{{ dep.cameraInterval }}</code>,
+    height: <code>{{ dep.cameraHeight }}</code>,
+    tilt: <code>{{ dep.cameraTilt }}</code>,
+    heading: <code>{{ dep.cameraHeading }}</code>
+  </dd>
+  <dt>Bait</dt>
+  <dd>
+    <code>{{ dep.baitUse }}</code>
+  </dd>
+</dl>
+
+{% assign event_ids = media | map: 'eventID' | uniq %}
+{% for event_id in event_ids %}
+  {% assign event_media = media | where: 'eventID', event_id %}
+  {% assign event_media_count = event_media | size %}
+  <h2 id="{{ event_id }}">Event: {{ event_id }}</h2>
+
+  <div id="carousel-{{ event_id }}" class="carousel slide carousel-fade" data-bs-ride="carousel" data-bs-keyboard="false" data-bs-interval="500">
+    <div class="carousel-inner">
+      {% for med in event_media %}
+        <div class="carousel-item{% if forloop.first %} active{% endif %}">
+          <img class="d-block w-100" src="{{ med.filePath }}" alt="{{ med.timestamp }}">
+          <div class="carousel-caption d-none d-md-block">
+            <p class="fs-1">{{ forloop.index }}</p>
+          </div>
+        </div>
+      {% endfor %}
+    </div>
+    <button class="carousel-control-prev" type="button" data-bs-target="#carousel-{{ event_id }}" data-bs-slide="prev">
+      <span class="carousel-control-prev-icon" aria-hidden="true"></span>
+      <span class="visually-hidden">Previous</span>
+    </button>
+    <button class="carousel-control-next" type="button" data-bs-target="#carousel-{{ event_id }}" data-bs-slide="next">
+      <span class="carousel-control-next-icon" aria-hidden="true"></span>
+      <span class="visually-hidden">Next</span>
+    </button>
+  </div>
+
+  <table class="table table-sm mt-4">
+    <colgroup>
+      <col width="6%">
+      <col width="47%">
+      <col width="47%">
+    </colgroup>
+    <thead>
+      <tr>
+        <th>File</th>
+        <th>Media observations</th>
+        <th>Event observations</th>
+      </tr>
+    </thead>
+    <tbody>
+      {% for med in event_media %}
+        {% assign med_id = med.mediaID %}
+        <tr>
+          <td>
+            {{ forloop.index }}
+          </td>
+          <td title="mediaID: {{ med_id }}">
+            {% assign media_obs = media_observations | where: 'mediaID', med_id %}
+            {% for obs in media_obs %}
+              <code>{{ obs.observationType }}</code>
+              {% if obs.observationType == 'animal' %}
+                <span class="badge rounded-pill bg-secondary">{{ obs.count }}</span>
+                <em>{{ obs.scientificName }}</em>
+                {% if obs.lifeStage and obs.sex %}
+                  ({{ obs.lifeStage }}, {{ obs.sex }})
+                {% elsif obs.lifeStage %}
+                  ({{ obs.lifeStage }})
+                {% elsif obs.sex %}
+                  ({{ obs.sex }})
+                {% endif %}
+              {% endif %}
+              {% if obs.classificationMethod == 'machine' %}
+                <span class="text-muted small">Classified by machine</span>    
+              {% endif %}
+              <br>
+            {% endfor %}
+          </td>
+          {% if forloop.first %}
+          <td title="eventID: {{ event_id }}" rowspan="{{ event_media_count }}">
+            {% assign event_obs = event_observations | where: 'eventID', event_id %}
+            {% for obs in event_obs %}
+              <code>{{ obs.observationType }}</code>
+              {% if obs.observationType == 'animal' %}
+                <span class="badge rounded-pill bg-secondary">{{ obs.count }}</span>
+                <em>{{ obs.scientificName }}</em>
+                {% if obs.lifeStage and obs.sex %}
+                  ({{ obs.lifeStage }}, {{ obs.sex }})
+                {% elsif obs.lifeStage %}
+                  ({{ obs.lifeStage }})
+                {% elsif obs.sex %}
+                  ({{ obs.sex }})
+                {% endif %}
+              {% endif %}
+              {% if obs.classificationMethod == 'machine' %}
+                <span class="text-muted small">Classified by machine</span>    
+              {% endif %}
+              <br>
+            {% endfor %}
+          </td>
+          {% endif %}
+        </tr>
+      {% endfor %}
+    </tbody>
+  </table>
+{% endfor %}

_layouts/profile.html

@@ -8,7 +8,7 @@
 {% assign properties1 = site.data[profile_file].allOf[1].properties %}
 {% assign required1 = site.data[profile_file].allOf[1].required %}
 
-<p class="small">Source: <a href="https://github.com/{{ site.github_username }}/blob/main/{{ profile_file }}.json"><code>{{ profile_file }}.json</code></a></p>
+<p class="small">Source: <a href="{{ site.github.repository_url }}/blob/main/{{ profile_file }}.json"><code>{{ profile_file }}.json</code></a></p>
 
 {% for p1_raw in properties1 %}
   {% assign p1_name = p1_raw[0] %}
@@ -25,9 +25,9 @@ <h2 id="{{ p1_id }}">
   {% if p1['skos:exactMatch'] %}
     <p class="small text-muted">Same as <a href="{{ p1['skos:exactMatch'] }}">{{ p1['skos:exactMatch'] }}</a></p>
   {% elsif p1['skos:narrowMatch'] %}
-    <p class="small text-muted">Narrower than <a href="{{ p1['skos:narrowMatch'] }}">{{ p1['skos:narrowMatch'] }}</a></p>
+    <p class="small text-muted">Broader than <a href="{{ p1['skos:narrowMatch'] }}">{{ p1['skos:narrowMatch'] }}</a></p>
   {% elsif p1['skos:broadMatch'] %}
-    <p class="small text-muted">Broader than <a href="{{ p1['skos:broadMatch'] }}">{{ p1['skos:broadMatch'] }}</a></p>
+    <p class="small text-muted">Narrower than <a href="{{ p1['skos:broadMatch'] }}">{{ p1['skos:broadMatch'] }}</a></p>
   {% endif %}
 
   {% if p1.properties %}
@@ -36,6 +36,9 @@ <h2 id="{{ p1_id }}">
   {% elsif p1.items.properties %}
     {% assign properties2 = p1.items.properties %}
     {% assign required2 = p1.items.required %}
+  {% elsif p1.items.oneOf[0].properties %}
+    {% assign properties2 = p1.items.oneOf[0].properties %}
+    {% assign required2 = p1.items.oneOf[0].required %}
   {% else %}
     {% assign properties2 = false %}
   {% endif %}
@@ -83,9 +86,9 @@ <h2 id="{{ p1_id }}">
             {% if p2['skos:exactMatch'] %}
               <span class="small text-muted">Same as <a href="{{ p2['skos:exactMatch'] }}">{{ p2['skos:exactMatch'] }}</a></span>
             {% elsif p2['skos:narrowMatch'] %}
-              <span class="small text-muted">Narrower than <a href="{{ p2['skos:narrowMatch'] }}">{{ p2['skos:narrowMatch'] }}</a></span>
+              <span class="small text-muted">Broader than <a href="{{ p2['skos:narrowMatch'] }}">{{ p2['skos:narrowMatch'] }}</a></span>
             {% elsif p2['skos:broadMatch'] %}
-              <span class="small text-muted">Broader than <a href="{{ p2['skos:broadMatch'] }}">{{ p2['skos:broadMatch'] }}</a></span>
+              <span class="small text-muted">Narrower than <a href="{{ p2['skos:broadMatch'] }}">{{ p2['skos:broadMatch'] }}</a></span>
             {% endif %}
           </td>
           <td>{{ p2.type }}</td>

_layouts/tables.html

@@ -10,7 +10,7 @@
 
   <h2 id="{{ table_schema_id }}">{{ table_schema.title }}</h2>
 
-  <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>
+  <p class="small">Source: <a href="{{ site.github.repository_url }}/blob/main/{{ table_schema_file }}.json"><code>{{ table_schema_file }}.json</code></a></p>
 
   {{ table_schema.description | markdownify }}
 
@@ -52,9 +52,9 @@ <h2 id="{{ table_schema_id }}">{{ table_schema.title }}</h2>
             {% if field['skos:exactMatch'] %}
               <span class="small text-muted">Same as <a href="{{ field['skos:exactMatch'] }}">{{ field['skos:exactMatch'] }}</a></span>
             {% elsif field['skos:narrowMatch'] %}
-              <span class="small text-muted">Narrower than <a href="{{ field['skos:narrowMatch'] }}">{{ field['skos:narrowMatch'] }}</a></span>
+              <span class="small text-muted">Broader than <a href="{{ field['skos:narrowMatch'] }}">{{ field['skos:narrowMatch'] }}</a></span>
             {% elsif field['skos:broadMatch'] %}
-              <span class="small text-muted">Broader than <a href="{{ field['skos:broadMatch'] }}">{{ field['skos:broadMatch'] }}</a></span>
+              <span class="small text-muted">Narrower than <a href="{{ field['skos:broadMatch'] }}">{{ field['skos:broadMatch'] }}</a></span>
             {% endif %}
           </td>
           <td>{{ field.type }}</td>

camtrap-dp-profile.json

@@ -26,41 +26,64 @@
         "resources": {
           "description": "See [Data Package specification](https://specs.frictionlessdata.io/data-package/#resource-information). Camtrap DP further requires each object to be a [Tabular Data Resource](https://specs.frictionlessdata.io/tabular-data-resource/) with a specific `name` and `schema`. See [Data](../data) for the requirements for those resources.",
           "minItems": 3,
-          "maxItems": 3,
           "items": {
-            "required": [
-              "schema",
-              "profile"
-            ],
-            "properties": {
-              "name": {
-                "description": "Identifier of the resource.",
-                "enum": [
-                  "deployments",
-                  "media",
-                  "observations"
-                ]
-              },
-              "profile": {
-                "const": "tabular-data-resource"
-              },
-              "schema": {
-                "description": "URL of the used Camtrap DP Table Schema version (e.g. `https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/deployments-table-schema.json`).",
-                "$ref": "#$defs/version",
+            "oneOf": [
+              {
                 "required": [
-                  "name"
+                  "name",
+                  "path",
+                  "profile",
+                  "schema"
                 ],
                 "properties": {
                   "name": {
+                    "description": "Identifier of the resource.",
                     "enum": [
                       "deployments",
                       "media",
                       "observations"
                     ]
+                  },
+                  "path": {
+                    "description": "Path or URL to the data file."
+                  },
+                  "profile": {
+                    "description": "[Profile](https://specs.frictionlessdata.io/profiles/) of the resource.",
+                    "enum": [
+                      "tabular-data-resource"
+                    ]
+                  },
+                  "schema": {
+                    "description": "URL of the used Camtrap DP Table Schema version (e.g. `https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/deployments-table-schema.json`).",
+                    "allOf": [
+                      {
+                        "$ref": "#$defs/version"
+                      },
+                      {
+                        "type": "string",
+                        "format": "uri"
+                      }
+                    ]
+                  }
+                }
+              },
+              {
+                "required": [
+                  "name"
+                ],
+                "properties": {
+                  "name": {
+                    "not": {
+                      "enum": [
+                        "deployments",
+                        "media",
+                        "observations"
+                      ]
+                    }
                   }
                 }
               }
-            }
+            ]
           }
         },
         "profile": {
@@ -80,7 +103,21 @@
           "description": "See [Data Package specification](https://specs.frictionlessdata.io/data-package/#title). Not to be confused with the title of the project that originated the package (`package.project.title`)."
         },
         "contributors": {
-          "description": "See [Data Package specification](https://specs.frictionlessdata.io/data-package/#contributors). Camtrap DP makes this a required property. Can include people and organizations."
+          "description": "See [Data Package specification](https://specs.frictionlessdata.io/data-package/#contributors). Camtrap DP makes this a required property and restricts `role` values. Can include people and organizations.",
+          "items": {
+            "properties": {
+              "role": {
+                "description": "Role of the contributor. Defaults to `contributor`.",
+                "enum": [
+                  "contact",
+                  "principalInvestigator",
+                  "rightsHolder",
+                  "publisher",
+                  "contributor"
+                ]
+              }
+            }
+          }
         },
         "description": {
           "description": "See [Data Package specification](https://specs.frictionlessdata.io/data-package/#description). Not to be confused with the description of the project that originated the package (`package.project.description`)."
@@ -167,11 +204,12 @@
             },
             "samplingDesign": {
               "description": "Type of a sampling design/layout. The values are based on Wearn & Glover-Kapfer (2017, <https://doi.org/10.13140/RG.2.2.23409.17767>), pages 80-82: `simple random`: random distribution of sampling locations; `systematic random`: random distribution of sampling locations, but arranged in a regular pattern; `clustered random`: random distribution of sampling locations, but clustered in arrays; `experimental`: non-random distribution aimed to study an effect, including the before-after control-impact (BACI) design; `targeted`: non-random distribution optimized for capturing specific target species (often using various bait types); `opportunistic`: opportunistic camera trapping (usually with a small number of cameras).",
+              "skos:broadMatch": "http://rs.tdwg.org/hc/terms/inventoryTypes",
               "type": "string",
               "enum": [
-                "simple random",
-                "systematic random",
-                "clustered random",
+                "simpleRandom",
+                "systematicRandom",
+                "clusteredRandom",
                 "experimental",
                 "targeted",
                 "opportunistic"
@@ -183,8 +221,8 @@
               "items": {
                 "type": "string",
                 "enum": [
-                  "motion detection",
-                  "time lapse"
+                  "motionDetection",
+                  "timeLapse"
                 ]
               },
               "uniqueItems": true,