v1.0

.github/workflows/jekyll.yml

@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
@@ -48,7 +48,7 @@ jobs:
           JEKYLL_ENV: production
       - name: Upload artifact
         # Automatically uploads an artifact from the './_site' directory by default
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
 
   # Deployment job
   deploy:

.github/workflows/validate-profile-and-schemas.yml

@@ -10,9 +10,9 @@ jobs:
   validate-profile-and-schemas:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: 3.9
       - name: Install dependencies

CITATION.cff

@@ -1,5 +1,4 @@
 cff-version: 1.2.0
-message: 'To cite "GeoLocator DP" in publications use:'
 type: software
 license: MIT
 title: GeoLocator Data Package
@@ -9,7 +8,17 @@ authors:
     email: rafnuss@gmail.com
     affiliation: Swiss Ornithological Institute
     orcid: https://orcid.org/0000-0002-8185-1020
+  - family-names: Capilla-Lasheras
+    given-names: Pablo
+    email: pablo.capilla@gvogelwarte.ch
+    affiliation: Swiss Ornithological Institute
+    orcid: https://orcid.org/0000-0001-6091-7089
+  - family-names: Desmet
+    given-names: Peter
+    email: peter.desmet@inbo.be
+    affiliation: Research Institute for Nature and Forest
+    orcid: https://orcid.org/0000-0002-8442-8025
 repository-code: https://github.com/rafnuss/geolocator-dp
-url: https://raphaelnussbaumer.com/GeoLocator-DP/
+url: https://geopressure.org/GeoLocator-DP/
 date-released: "2024-12-02"
 doi: 10.5281/zenodo.14258411

README.md

@@ -1,94 +1,46 @@
----
-title: GeoLocator DP
-background: /assets/home.png
-permalink: /
-description: Data exchange format for geolocator data
----
+# GeoLocator DP
 
-**GeoLocator Data Package** (GeoLocator DP) is a data exchange format for geolocator data. It follows the [Data Package standard](https://datapackage.org/standard/data-package/) for structuring the data.
+GeoLocator DP is a Data Package profile for geolocator data (raw measurements, field observations, and optional GeoPressureR trajectory outputs).
 
-## Structure
+## Documentation
 
-A GeoLocator Data Package is organized into three components: (1) the project metadata, (2) the core resources containing the main dataset, and (3) optional trajectory data generated with the [GeoPressure suite](https://raphaelnussbaumer.com/GeoPressureManual/#the-geopressure-suite).
+- Website: https://geopressure.org/GeoLocator-DP/
+- GeoLocator Manual: https://raphaelnussbaumer.com/GeoPressureManual/geolocator-intro.html
+- GeoLocatoR package: https://raphaelnussbaumer.com/GeoLocatoR/
 
-### 1. Metadata
+## Repository Contents
 
-The description of the project and the data is contained in [`datapackage.json`](https://raphaelnussbaumer.com/GeoLocator-DP/datapackage/).
+- `geolocator-dp-profile.json`: GeoLocator DP package profile
+- `*-table-schema.json`: table schemas for core and GeoPressureR resources
+- `pages/`: website pages rendered by Jekyll
+- `example/`: example CSV resources
+- `tests/`: validation tests
 
-| File                                                                           | Description                                                                                                                                                                                                      |
-| ------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| [`datapackage.json`](https://raphaelnussbaumer.com/GeoLocator-DP/datapackage/) | List of the project's metadata, such as the package's title, licenses, contributors, etc., as well as a list of the data [`resources`](https://datapackage.org/standard/data-resource/) that make up the package |
+## Local Development
 
-### 2. Core Resources
+Install Ruby dependencies:
 
-The core GeoLocator DP resources consist of the raw geolocator data. These `resources` can be generated without any analysis of the geolocator data.
+```bash
+bundle install
+```
 
-| File                                                                                 | Description                                                                                           |
-| ------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------- |
-| [`tags.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/core/tags/)                 | Table of devices used in the study. We assume that a `tag` is only used once on a single animal.      |
-| [`measurements.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/core/measurements/) | Table with the raw measurements of all sensors (e.g., light, pressure, ...) for all tags.             |
-| [`observations.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/core/observations/) | Table with the field observations associated with tags such as equipment, retrieval, or other events. |
+Run the website locally with live reload:
 
-### 3. GeoPressureR Resources
+```bash
+bundle exec jekyll serve --livereload --incremental
+```
 
-The GeoPressureR extension consists of optional trajectory data generated through the [GeoPressureR workflow analysis](https://raphaelnussbaumer.com/GeoPressureManual/geopressuretemplate-workflow.html).
+Create a production-style build:
 
-| File                                                                                          | Description                                                                          |
-| --------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ |
-| [`staps.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/geopressurer/staps)                 | Table of the stationary periods of all tags.                                         |
-| [`paths.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/geopressurer/paths)                 | Table of the trajectory of all tags, typically most likely path or simulation paths. |
-| [`edges.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/geopressurer/edges)                 | Table containing the flight information of the edges associated with the paths.      |
-| [`twilights.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/geopressurer/twilights)         | Table of the twilights estimated from light data for all tags.                       |
-| [`pressurepaths.csv`](https://raphaelnussbaumer.com/GeoLocator-DP/geopressurer/pressurepaths) | Table of pressure-based paths.                                                       |
+```bash
+JEKYLL_ENV=production bundle exec jekyll build
+```
 
-## Where to find and explore GeoLocator Data Packages
+Run validation tests:
 
-<table>
-    <tr style="border-top-width: 1px;">
-        <td>
-            <a href="https://zenodo.org/communities/geolocator-dp/"><img src="assets/logo.png" width="100px" alt="GeoLocator DP logo"/> </a>
-        </td>
-        <td>
-            You'll be able to find all GeoLocator Data Packages in the <a href="https://zenodo.org/communities/geolocator-dp/">GeoLocator Data Package Zenodo Community</a>. Once you've published your data package, make sure to <a href="https://help.zenodo.org/docs/share/submit-to-community/">submit it to the community</a>.
-        </td>
-    </tr>
-    <tr>
-        <td>
-            <a href="https://raphaelnussbaumer.com/GeoLocatorExplorer/"><img src="assets/logo_geolocatorexplorer.svg" width="100px" alt="GeoLocatorExplorer logo"/> </a>
-        </td>
-        <td>
-            Explore the most likely trajectories of all existing data packages on a 3D map with <a href="https://raphaelnussbaumer.com/GeoLocatorExplorer/">GeoLocatorExplorer</a>.
-        </td>
-    </tr>
-</table>
-
-## Ecosystem
-
-<table>
-    <tr style="border-top-width: 1px;">
-        <td>
-            <a href="https://raphaelnussbaumer.com/GeoPressureManual/geolocator-intro.html"><img src="assets/cover_geopressuremanual.png" width="100px" alt="GeoPressureManual logo"/></a>
-        </td>
-        <td>
-            The <a href="https://raphaelnussbaumer.com/GeoPressureManual/geolocator-intro.html">Geolocator Manual</a> R book has a dedicated part on the use of the GeoLocator Data Package. This is a great place to start learning more about how to use it with your GeoPressureTemplate project.
-        </td>
-    </tr>
-    <tr>
-        <td>
-            <a href="https://raphaelnussbaumer.com/GeoLocatoR/"><img src="assets/logo_geolocator.png" width="100px" alt="GeoLocatoR logo"/></a>
-        </td>
-        <td>
-            The <a href="https://raphaelnussbaumer.com/GeoLocatoR/">GeoLocatoR</a> R package is designed to handle GeoLocator DP: creating a DP, adding resources, writing a DP, and reading a DP. It is essentially an extension of the <a href="https://docs.ropensci.org/frictionless/">frictionlessr</a> package for geolocator data.
-        </td>
-    </tr>
-    <tr>
-        <td><a href="https://raphaelnussbaumer.com/GeoPressureR/"><img src="assets/logo_geopressurer.png" width="100px" alt="GeoPressureR logo"/></a></td>
-        <td>
-            <a href="https://raphaelnussbaumer.com/GeoPressureR/">GeoPressureR</a> is the main package to analyze geolocator data. Once a GeoLocator Data Package is created, GeoPressureR is our recommended software to read the data into R and analyze the data.
-        </td>
-    </tr>
-</table>
-
-## How to Cite
-
-> Nussbaumer, R. (2024). GeoLocator-DP: Data exchange format for multi-sensor geolocator. Zenodo. [10.5281/zenodo.14258411](https://doi.org/10.5281/zenodo.14258411)
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -r tests/requirements.txt
+python tests/validate_profile_and_schemas.py
+```

_config.yml

@@ -1,7 +1,7 @@
 # SITE SETTINGS
 title: GeoLocator DP
 author: GeoLocator Development Team
-url: https://raphaelnussbaumer.com
+url: https://geopressure.org
 baseurl: /GeoLocator-DP
 
 # THEME SETTINGS

_data/footer.yml

@@ -9,7 +9,7 @@
 
 columns:
   - description: > # E.g. funding acknowledgement. Can be Markdown
-      This website and Data Package extension were greatly inspired from [Camtrap DP](https://camtrap-dp.tdwg.org/) and the website is using the [petridish](https://peterdesmet.com/petridish/) jekyll theme.
+      This website and Data Package extension were inspired from [Camtrap DP](https://camtrap-dp.tdwg.org/) and the website is using the [petridish](https://peterdesmet.com/petridish/) jekyll theme.
 
 # Small print license statement to add at the bottom of the footer. Can be Markdown
 # Will be prefixed by "© {{ site.author }}" if defined in _config.yml

_data/measurements-table-schema.json

@@ -0,0 +1,87 @@
+{
+  "name": "measurements",
+  "title": "Measurements",
+  "description": "`measurements.csv` is a [tabular data](https://datapackage.org/standard/glossary/#tabular-data) resource from a GeoLocator Data Package containing raw data from sensors on all tags.\n\n{:.alert .alert-warning}\nNote that data from all sensors and all tags are contained in a single table!",
+  "$schema": "https://datapackage.org/profiles/2.0/tableschema.json",
+  "fields": [
+    {
+      "name": "tag_id",
+      "description": "Unique identifier of the tag. Foreign key to [`tags.tag_id`](/GeoLocator-DP/core/tags#tag_id).",
+      "type": "string",
+      "constraints": {
+        "required": true
+      },
+      "example": "18LX"
+    },
+    {
+      "name": "sensor",
+      "description": "Sensor type.\n - `light`: Light-level values measured by a solar geolocator. Range and units may vary by provider and tag settings. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000139/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000139/</a></span>\n - `pressure`: Atmospheric pressure in hPa (or mbar). <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000055/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000055/</a></span>\n - `activity`: Measure of movement performed by the bird, computed from acceleration sensors. Range and computation method may vary by tag provider, model, settings, and placement on the animal. In general, higher values indicate more activity. Typically computed as the cumulative sum of the absolute difference of acceleration along the z-axis. See [doi:10.1186/s40462-018-0137-1](https://doi.org/10.1186/s40462-018-0137-1) (SOI), [doi:10.1111/jav.01068](https://doi.org/10.1111/jav.01068) (Lund), and the [migratetech report](https://www.migratetech.co.uk/IntigeoSummary.pdf) for more details. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000114/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000114/</a></span>\n - `mean_acceleration_z`: Mean acceleration along the z-axis, computed from acceleration sensors. Mainly used by SOI devices. This metric is sometimes used as a proxy for pitch and was named `pitch` in GeoLocator DP versions earlier than v1.0.\n - `temperature_external`: Temperature measured by the tag sensor pointing outward from the animal (air temperature). This typically corresponds to the main external temperature sensor. Units: degrees Celsius. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000104/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000104/</a></span>\n - `temperature_internal`: Temperature measured by the tag sensor located between the tag and the animal (body temperature). Units: degrees Celsius. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000256/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000256/</a></span>\n - `acceleration_x`: Raw acceleration values provided by the tag for the X axis. Units: m/s^2. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000006/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000006/</a></span>\n - `acceleration_y`: Raw acceleration values provided by the tag for the Y axis. Units: m/s^2. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000007/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000007/</a></span>\n - `acceleration_z`: Raw acceleration values provided by the tag for the Z axis. Units: m/s^2. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000008/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000008/</a></span>\n - `magnetic_x`: Magnetic field strength measured by the magnetometer for the X axis. Units: microtesla. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000258/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000258/</a></span>\n - `magnetic_y`: Magnetic field strength measured by the magnetometer for the Y axis. Units: microtesla. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000259/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000259/</a></span>\n - `magnetic_z`: Magnetic field strength measured by the magnetometer for the Z axis. Units: microtesla. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000260/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000260/</a></span>\n - `wet_count`: Wet count during a measurement interval from the wet-dry sensor. Units are usually device-specific. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000213/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000213/</a></span>\n - `conductivity`: Conductivity measured by the wet-dry sensor. Unit varies by model. <br/><span class='small text-muted'>Same as <a href='https://vocab.nerc.ac.uk/collection/MVB/current/MVB000071/'>https://vocab.nerc.ac.uk/collection/MVB/current/MVB000071/</a></span>",
+      "type": "string",
+      "constraints": {
+        "required": true,
+        "enum": [
+          "light",
+          "pressure",
+          "activity",
+          "mean_acceleration_z",
+          "temperature_internal",
+          "temperature_external",
+          "acceleration_x",
+          "acceleration_y",
+          "acceleration_z",
+          "magnetic_x",
+          "magnetic_y",
+          "magnetic_z",
+          "wet_count",
+          "conductivity"
+        ]
+      },
+      "skos:relatedMatch": "https://vocab.nerc.ac.uk/collection/MVB/current/MVB000170/",
+      "example": "pressure"
+    },
+    {
+      "name": "datetime",
+      "description": "Date and time of the measurement. Accepts any valid [ISO 8601](https://wikipedia.org/wiki/ISO_8601) datetime string, including datetime in local time (`YYYY-MM-DDThh:mm`), in UTC (`YYYY-MM-DDThh:mmZ`) or any specific timezone (`YYYY-MM-DDThh:mm+hh:mm`).",
+      "type": "datetime",
+      "constraints": {
+        "required": true
+      },
+      "example": "2020-04-01T22:00:00Z",
+      "skos:closeMatch": "http://vocab.nerc.ac.uk/collection/MVB/current/MVB000200"
+    },
+    {
+      "name": "value",
+      "description": "Value of the measurement taken by the sensor.",
+      "type": "number",
+      "constraints": {
+        "required": true
+      },
+      "example": "12.3"
+    },
+    {
+      "name": "label",
+      "description": "Labeling of pressure and acceleration data according to the [labeling chapter of the GeoPressureManual](https://raphaelnussbaumer.com/GeoPressureManual/labelling-tracks.html).",
+      "type": "string",
+      "constraints": {
+        "required": false,
+        "pattern": "^(flight|discard|elev_\\d+|)$"
+      },
+      "example": "elev_23",
+      "skos:relatedMatch": [
+        "https://vocab.nerc.ac.uk/collection/MVB/current/MVB000156",
+        "https://vocab.nerc.ac.uk/collection/MVB/current/MVB000157"
+      ]
+    }
+  ],
+  "missingValues": ["", "NA"],
+  "foreignKeys": [
+    {
+      "fields": "tag_id",
+      "reference": {
+        "resource": "tags",
+        "fields": "tag_id"
+      }
+    }
+  ],
+  "fieldsMatch": ["superset"]
+}

_data/navigation.yml

@@ -2,8 +2,8 @@
 
 - text: Home
   href: /
-- text: Datapackage
-  href: /datapackage/
+- text: Overview
+  href: /schema-overview/
 - text: Core
   menu:
     - text: Tags
@@ -24,5 +24,5 @@
       href: /geopressurer/edges/
     - text: Pressurepaths
       href: /geopressurer/pressurepaths/
-- text: "GitHub"
-  href: "https://github.com/rafnuss/geolocator-dp"
+- text: Curation
+  href: /curation/

_includes/footer.html

@@ -0,0 +1,14 @@
+<footer class="d-print-none">
+  <div class="container">
+    <div class="small mt-2 text-center">
+      {% if site.author %}
+        <p>© {{ site.author }}</p>
+      {% endif %}
+      <p><a href="https://github.com/rafnuss/geolocator-dp">GitHub Repository</a></p>
+      {% if site.data.footer.license %}
+        <p>{{ site.data.footer.license | markdownify | remove: '<p>' | remove: '</p>' }}</p>
+      {% endif %}
+      <p>Inspired by <a href="https://camtrap-dp.tdwg.org/">Camtrap DP</a> and built with <a href="https://peterdesmet.com/petridish/">Petridish</a>.</p>
+    </div>
+  </div>
+</footer>