GBIF EML Profile

pygeometa/schemas/__init__.py

@@ -56,6 +56,7 @@
     'cwl': 'pygeometa.schemas.cwl.CWLOutputSchema',
     'csvw': 'pygeometa.schemas.csvw.CSVWOutputSchema',
     'dcat': 'pygeometa.schemas.dcat.DCATOutputSchema',
+    'gbif-eml': 'pygeometa.schemas.gbif_eml.GBIF_EMLOutputSchema',
     'iso19139': 'pygeometa.schemas.iso19139.ISO19139OutputSchema',
     'iso19139-2': 'pygeometa.schemas.iso19139_2.ISO19139_2OutputSchema',
     'iso19139-hnap': 'pygeometa.schemas.iso19139_hnap.ISO19139HNAPOutputSchema',  # noqa

pygeometa/schemas/gbif_eml/__init__.py

@@ -0,0 +1,237 @@
+# =================================================================
+#
+# Terms and Conditions of Use
+#
+# Unless otherwise noted, computer program source code of this
+# distribution # is covered under Crown Copyright, Government of
+# Canada, and is distributed under the MIT License.
+#
+# The Canada wordmark and related graphics associated with this
+# distribution are protected under trademark law and copyright law.
+# No permission is granted to use them outside the parameters of
+# the Government of Canada's corporate identity program. For
+# more information, see
+# http://www.tbs-sct.gc.ca/fip-pcim/index-eng.asp
+#
+# Copyright title to all 3rd party software distributed with this
+# software is held by the respective copyright holders as noted in
+# those files. Users are asked to read the 3rd Party Licenses
+# referenced with those assets.
+#
+# Copyright (c) 2026 Niccolò Cantù
+#
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation
+# files (the "Software"), to deal in the Software without
+# restriction, including without limitation the rights to use,
+# copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following
+# conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+# =================================================================
+
+from pathlib import Path
+import re
+
+from bs4 import BeautifulSoup
+import pycountry
+
+from pygeometa.schemas.base import BaseOutputSchema
+
+THISDIR = Path(__file__).parent
+
+
+def text_or_null(node, strip=False):
+    if not node:
+        return None
+
+    if strip:
+        return node.text.strip()
+
+    return node.text
+
+
+def text_or_empty(node, strip=False):
+    if not node:
+        return ''
+
+    if strip:
+        return node.text.strip()
+
+    return node.text
+
+
+def scrub_dict(d):
+    if type(d) is dict:
+        return dict(
+            (k, scrub_dict(v))
+            for k, v in d.items()
+            if v is not None and scrub_dict(v) is not None
+        )
+    else:
+        return d
+
+
+def to_contact_role(node, role, mapped_role=None):
+    if not mapped_role:
+        mapped_role = role
+
+    for idx, contact in enumerate(node.find_all(role)):
+        name = f'{text_or_empty(contact.find("surName"))}, '
+        name += text_or_empty(contact.find('givenName'))
+        org = text_or_empty(contact.find('organizationName'))
+        yield (
+            mapped_role + (f'_{idx}' if idx else ''),
+            {
+                'organization': org,
+                'individualname': name,
+                'positionname': text_or_empty(contact.find('positionName'))
+                or text_or_empty(contact.find('role')),
+                'phone': '',
+                'url': '',
+                'fax': '',
+                'address': '',
+                'city': '',
+                'administrativearea': '',
+                'postalcode': '',
+                'country': text_or_empty(contact.find('country')),
+                'email': text_or_empty(contact.find('electronicMailAddress'))
+            },
+        )
+
+
+class GBIF_EMLOutputSchema(BaseOutputSchema):
+    def __init__(self):
+        super().__init__('gbif-eml', 'EML - GBIF profile', 'xml', THISDIR)
+
+    def import_(self, metadata):
+        soup = BeautifulSoup(metadata, features='lxml-xml')
+        dataset = soup.find('dataset')
+        mcf = {
+            'mcf': {
+                'version': 1,
+            },
+            'metadata': {
+                'charset': 'utf8',
+                'hierarchylevel': 'dataset',
+                'datestamp': text_or_null(dataset.find('pubDate'), strip=True)
+                or '$date$',
+            },
+            'identification': {},
+            'contact': {},
+            'distribution': {}
+        }
+
+        for identifier in dataset.find_all('alternateIdentifier'):
+            mcf['metadata']['identifier'] = text_or_null(identifier)
+
+        if language := dataset.find('language'):
+            lang = text_or_null(language)
+            if lang and pycountry.languages.get(alpha_3=lang):
+                mcf['metadata']['language'] = pycountry.languages.get(
+                    alpha_3=lang
+                ).alpha_2
+
+        idf = mcf['identification']
+
+        idf['title'] = text_or_null(dataset.find('title'))
+        idf['abstract'] = text_or_null(dataset.find('abstract'))
+
+        if intellectual_rights := dataset.find('intellectualRights'):
+            url = (
+                intellectual_rights.find('ulink')['url']
+                if intellectual_rights.find('ulink')
+                else None
+            )
+            idf['rights'] = {
+                'name': text_or_null(intellectual_rights.find('citetitle')),
+                'url': url
+            }
+
+        idf['url'] = text_or_null(dataset.find('alternateIdentifier'))
+        idf['status'] = 'completed'
+
+        idf['maintenancefrequency'] = (
+            text_or_null(dataset.find('maintenanceUpdateFrequency'))
+            or 'unknown'
+        )
+
+        idf['dates'] = {
+            'publication': text_or_null(dataset.find('pubDate'), strip=True)
+        }
+        idf['extents'] = {}
+
+        if coords := dataset.find('boundingCoordinates'):
+            idf['extents']['spatial'] = [{}]
+            spatial = idf['extents']['spatial'][0]
+
+            spatial['bbox'] = [
+                float(coords.find('westBoundingCoordinate').text),
+                float(coords.find('southBoundingCoordinate').text),
+                float(coords.find('eastBoundingCoordinate').text),
+                float(coords.find('northBoundingCoordinate').text)
+            ]
+
+            spatial['crs'] = 4326
+            spatial['description'] = text_or_null(
+                dataset.find('geographicDescription')
+            )
+
+        idf['keywords'] = {}
+
+        ct = mcf['contact']
+
+        for r, obj in to_contact_role(dataset, 'contact', 'pointOfContact'):
+            ct[r] = obj
+
+        for r, obj in to_contact_role(
+            dataset, 'metadataProvider', 'distributor'
+        ):
+            ct[r] = obj
+
+        for r, obj in to_contact_role(dataset, 'creator'):
+            ct[r] = obj
+
+        for r, obj in to_contact_role(
+            dataset, 'personnel', 'projectPersonnel'
+        ):
+            ct[r] = obj
+
+        for idx, keyword_set in enumerate(dataset.find_all('keywordSet')):
+            thesaurus = text_or_null(keyword_set.find('keywordThesaurus'))
+            match = re.search(r'(?P<url>https?://[^\s]+)', thesaurus)
+            definition = match.group('url') if match else None
+
+            idf['keywords'][f'default-{idx}'] = {
+                'keywords': [
+                    text_or_null(kw) for kw in keyword_set.find_all('keyword')
+                ],
+                'vocabulary': {'name': thesaurus, 'url': definition},
+            }
+
+        mcf['spatial'] = {'datatype': 'vector', 'geomtype': 'composite'}
+
+        mcf['distribution'] = {
+            'file': {
+                'url': idf['url'],
+                'type': 'WWW:LINK',
+                'function': 'information',
+                'description': '',
+                'name': 'Darwin Core Archive'
+            }
+        }
+
+        return scrub_dict(mcf)

pygeometa/schemas/gbif_eml/main.j2

@@ -0,0 +1,150 @@
+<eml:eml xmlns:eml="eml://ecoinformatics.org/eml-2.1.1" xmlns:dc="http://purl.org/dc/terms/"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.1 http://rs.gbif.org/schema/eml-gbif-profile/1.1/eml.xsd"
+    packageId="{{ record['metadata']['dataseturi'] }}" system="http://gbif.org"
+    scope="system" xml:lang="{{ record['identification']['language'] }}">
+
+    <dataset>
+        <alternateIdentifier>{{ record['identification'].get('doi') }}</alternateIdentifier>
+        <title xml:lang="{{ record['identification']['language'] }}">{{ record['identification']['title'] }}</title>
+        {#
+        <!--creator>
+            {% include 'person.j2' %}
+        </creator>
+        <creator>
+            {% include 'person.j2' %}
+        </creator>
+        <metadataProvider>
+            {% include 'person.j2' %}
+        </metadataProvider-->
+        #}
+        <pubDate>
+            {{ record['identification']['dates']['publication'] }}
+        </pubDate>
+        <language>{{ record['identification']['language'] }}</language>
+        <abstract>
+            <para>{{ record['identification']['abstract'] }}</para>
+        </abstract>
+        {% for group, keywords in record['identification']['keywords'].items() %}
+        <keywordSet>
+            {% for kw in keywords['keywords'] %}
+            <keyword>{{ kw }}</keyword>
+            {% endfor %}
+            <keywordThesaurus>{{ keywords['vocabulary']['name'] }}: {{ keywords['vocabulary']['url'] }}</keywordThesaurus>
+        </keywordSet>
+        {% endfor%}
+        <intellectualRights>
+            <para>This work is licensed under a <ulink url="{{ record['identification']['rights']['url'] }}">
+                    <citetitle>{{ record['identification']['rights']['name'] }}</citetitle>
+                </ulink>.</para>
+        </intellectualRights>
+        <distribution scope="document">
+            <online>
+                {% for key, value in record['distribution'].items() %}
+                <url function="{{ value['function'] }}">{{ value['url' ]}}</url>
+                {% endfor %}
+            </online>
+        </distribution>
+        {% set extents = record['identification']['extents'] %}
+        {% set bbox = extents['spatial'][0]['bbox'] %}
+        <coverage>
+            <geographicCoverage>
+                <geographicDescription>{{ extents['spatial'][0]['description'] }}</geographicDescription>
+                <boundingCoordinates>
+                    <westBoundingCoordinate>{{ bbox[0] }}</westBoundingCoordinate>
+                    <eastBoundingCoordinate>{{ bbox[1] }}</eastBoundingCoordinate>
+                    <northBoundingCoordinate>{{ bbox[2] }}</northBoundingCoordinate>
+                    <southBoundingCoordinate>{{ bbox[3] }}</southBoundingCoordinate>
+                </boundingCoordinates>
+            </geographicCoverage>
+            {% if 'temporal' in extents %}
+            <temporalCoverage>
+                <rangeOfDates>
+                    <beginDate>
+                        <calendarDate>{{ extents['temporal'][0]['begin'] }}</calendarDate>
+                    </beginDate>
+                    {% if extents['temporal'][0]['end'] %}
+                    <endDate>
+                        <calendarDate>{{ extents['temporal'][0]['end'] }}</calendarDate>
+                    </endDate>
+                    {% endif %}
+                </rangeOfDates>
+            </temporalCoverage>
+            {% endif %}
+            <taxonomicCoverage>
+                <generalTaxonomicCoverage>
+                </generalTaxonomicCoverage>
+                <taxonomicClassification>
+                    <taxonRankName></taxonRankName>
+                    <taxonRankValue></taxonRankValue>
+                    <commonName></commonName>
+                </taxonomicClassification>
+            </taxonomicCoverage>
+        </coverage>
+        <maintenance>
+            <description>
+                <para />
+            </description>
+            <maintenanceUpdateFrequency></maintenanceUpdateFrequency>
+        </maintenance>
+
+        {#
+        <contact>
+            {% include 'person.j2' %}
+        </contact>
+        <methods>
+            <methodStep>
+                <description>
+                    <para></para>
+                </description>
+            </methodStep>
+            <sampling>
+                <studyExtent>
+                    <description>
+                        <para>
+                        </para>
+                    </description>
+                </studyExtent>
+                <samplingDescription>
+                    <para></para>
+                </samplingDescription>
+            </sampling>
+            <qualityControl>
+                <description>
+                    <para></para>
+                </description>
+            </qualityControl>
+        </methods>
+        <project>
+            <title></title>
+            <personnel>
+                {% include 'person.j2' %}
+                <role />
+            </personnel>
+            <abstract>
+                <para></para>
+            </abstract>
+            <funding>
+                <para>Artsdatabanken</para>
+            </funding>
+            <studyAreaDescription>
+                <descriptor name="generic" citableClassificationSystem="false">
+                    <descriptorValue></descriptorValue>
+                </descriptor>
+            </studyAreaDescription>
+        </project>
+         #}
+    </dataset>
+    {#
+    <additionalMetadata>
+        <metadata>
+            <gbif>
+                <dateStamp></dateStamp>
+                <hierarchyLevel>dataset</hierarchyLevel>
+                <citation></citation>
+                <resourceLogoUrl></resourceLogoUrl>
+            </gbif>
+        </metadata>
+    </additionalMetadata>
+    #}
+</eml:eml>