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541 | class DwcDerivativeGenerator(BaseDerivativeGenerator):
name = 'dwc'
extension = 'zip'
def __init__(
self,
output_dir,
fields,
query,
resource_id=None,
core_extension_name=None,
extension_names=None,
extension_map=None,
id_field='_id',
eml_title=None,
eml_abstract=None,
**format_args,
):
super(DwcDerivativeGenerator, self).__init__(
output_dir, fields, query, resource_id, **format_args
)
self._id_field = id_field
self._eml_title = eml_title
self._eml_abstract = eml_abstract
self._build_dir_name = uuid4().hex
self._build_dir = os.path.join(self.output_dir, self._build_dir_name)
os.mkdir(self._build_dir)
# LOAD THE SCHEMA
schema_args = {}
# there can be maximum one core extension
core_extension_name = core_extension_name or toolkit.config.get(
'ckanext.versioned_datastore.dwc_core_extension_name'
)
if (
core_extension_name is not None
and core_extension_name.lower() in urls.core_extensions
):
core_ext_url = urls.core_extensions.get(core_extension_name.lower())
schema_args['core_extension_url'] = core_ext_url
# there can be multiple non-core extensions, separated by commas in ckan.ini or supplied as
# a list in the request args
if extension_names is None:
extension_names = [
e.strip().lower()
for e in toolkit.config.get(
'ckanext.versioned_datastore.dwc_extension_names', ''
).split(',')
]
# the fields used by the extension can also be overridden by request args
extension_map = extension_map or {}
ext_urls = []
for e in extension_names:
ext = urls.extensions.get(e)
if not ext:
continue
fields = extension_map.get(e)
if fields is not None and isinstance(fields, list):
ext.fields = fields
if ext.fields: # no point in adding it if no fields are defined
ext_urls.append(ext)
if len(ext_urls) > 0:
schema_args['extension_urls'] = ext_urls
self.schema = Schema.load(
toolkit.config.get('ckanext.versioned_datastore.dwc_schema_cache'),
**schema_args,
)
# set up file paths & divide fields between core/extensions
self._core_file_name = f'{self.schema.row_type_name.lower()}.csv'
self.file_paths = {'core': os.path.join(self._build_dir, self._core_file_name)}
root_field_names = set([f.split('.')[0] for f in self.all_fields])
all_ext_field_names = [
item for ext in self.schema.extensions for item in ext.location.fields
]
dataset_fields = [
f
for f in root_field_names
if f not in all_ext_field_names and f in self.schema.props
]
self.fields = {
'core': ['_id'] + sorted(list(set(utils.standard_fields + dataset_fields)))
}
for e in self.schema.extensions:
self.file_paths[e.name] = os.path.join(
self._build_dir, f'{e.name.lower()}.csv'
)
subfields = [
f.split('.')[-1]
for f in self.all_fields
if f.split('.')[0] in e.location.fields
]
potential_fields = self.schema.extension_props[e.name]
ext_field_names = ['_id'] + list(
set([f for f in subfields if f in potential_fields])
)
self.fields[e.name] = ext_field_names
# this will contain csv writers for each component csv
self.writers = {}
# add meta and eml paths
self.file_paths['_meta'] = os.path.join(self._build_dir, 'meta.xml')
self.file_paths['_eml'] = os.path.join(self._build_dir, 'eml.xml')
# counts number of rows written
self.rows_written = 0
def __exit__(self, *args, **kwargs):
super(DwcDerivativeGenerator, self).__exit__(*args, **kwargs)
shutil.make_archive(
os.path.join(self.output_dir, os.path.splitext(self.output_name)[0]),
'zip',
self._build_dir,
)
def setup(self):
if not self._opened:
raise Exception('Files should be open.')
self.writers = {
k: csv.DictWriter(self.files[k], self.fields[k], dialect='unix')
for k in self.fields
}
# headers are written in .validate()
super(DwcDerivativeGenerator, self).setup()
def validate(self, record):
if 'type' in record and record['type'] not in utils.valid_types:
self.writers['core'].fieldnames = [
f for f in self.fields['core'] if f != 'type'
]
for k, writer in self.writers.items():
writer.writeheader()
super(DwcDerivativeGenerator, self).validate(record)
def finalise(self):
self.files['_meta'].write(self.make_meta())
self.files['_eml'].write(self.make_eml())
self.writers = {}
def cleanup(self):
try:
shutil.rmtree(self._build_dir)
except FileNotFoundError:
pass
def _write(self, record):
core_row, ext_rows = self._extract_record(record)
self.writers['core'].writerow(core_row)
for e, rows in ext_rows.items():
for row in rows:
self.writers[e].writerow(row)
self.rows_written += 1
def _extract_record(self, record):
"""
Transform the data in a single row into the required format. Separates extension
fields from core fields and filters out any fields that don't match the schema.
:param record: the row of data
:returns: core row (dict), extension rows keyed on extension name (dict of lists
of dicts)
"""
core = {}
ext = {}
dynamic_properties = {}
if self._id_field not in record:
raise Exception(f'Record does not have ID field {self._id_field}')
record_id = record.get(self._id_field)
core['_id'] = record_id
extension_map = {}
for e in self.schema.extensions:
for f in e.location.fields:
extension_map[f] = e.name
def _serialise_value(field_value):
# implement custom serialisation for field values, e.g. pipe-delimit lists
if isinstance(field_value, list):
return ' | '.join(
[str(subvalue) for subvalue in field_value if subvalue is not None]
)
else:
return field_value
for k, v in record.items():
if k in extension_map:
ext_props = self.writers[extension_map[k]].fieldnames
def _extract_ext(subdict):
props = {'_id': record_id}
for ek, ev in subdict.items():
if ek in ext_props and ek != '_id':
props[ek] = _serialise_value(ev)
return props
if isinstance(v, list):
ext_extracted = [_extract_ext(x) for x in v]
elif isinstance(v, dict):
ext_extracted = [_extract_ext(v)]
elif v is None:
# skip if empty
ext_extracted = []
else:
ext_extracted = [_extract_ext({k: v})]
ext[extension_map[k]] = ext_extracted
else:
if k in self.writers['core'].fieldnames:
core[k] = _serialise_value(v)
else:
dynamic_properties[k] = _serialise_value(v)
core['dynamicProperties'] = json.dumps(dynamic_properties)
return core, ext
def make_meta(self):
"""
Create the xml text content of the metafile.
:returns: xml string
"""
nsmap = utils.NSMap(xsi=urls.XMLUrls.xsi, xs=urls.XMLUrls.xs)
root = etree.Element(
'archive',
nsmap=nsmap,
attrib={
'xmlns': urls.TDWGUrls.xmlns,
'metadata': 'eml.xml',
nsmap.ns('xsi', 'schemaLocation'): ' '.join(
[urls.TDWGUrls.xmlns, urls.TDWGUrls.metadata]
),
},
)
attributes = {
'encoding': 'UTF-8',
'linesTerminatedBy': '\n',
'fieldsTerminatedBy': ',',
'fieldsEnclosedBy': '"',
'ignoreHeaderLines': '1',
}
core = etree.SubElement(
root, 'core', rowType=self.schema.row_type, **attributes
)
core_files = etree.SubElement(core, 'files')
core_files_location = etree.SubElement(core_files, 'location')
core_files_location.text = self._core_file_name
etree.SubElement(core, 'id', index='0')
for i, c in enumerate(self.writers['core'].fieldnames):
if c == '_id':
continue
prop = self.schema.props.get(c)
if prop is None:
continue
etree.SubElement(core, 'field', index=str(i), term=prop.iri)
for e in self.schema.extensions:
ext_root = etree.SubElement(
root, 'extension', rowType=e.row_type, **attributes
)
ext_files = etree.SubElement(ext_root, 'files')
ext_files_location = etree.SubElement(ext_files, 'location')
ext_files_location.text = f'{e.name.lower()}.csv'
etree.SubElement(ext_root, 'coreid', index='0')
ext_props = self.schema.extension_props[e.name]
for i, c in enumerate(self.writers[e.name].fieldnames):
if c == '_id':
continue
etree.SubElement(
ext_root, 'field', index=str(i), term=ext_props.get(c).iri
)
return etree.tostring(root, pretty_print=True).decode()
def make_eml(self):
"""
Create the xml text content of the resource metadata file.
Tries to use some sensible defaults and get information from other relevant
plugins where available, but there's still the potential for errors or silly
data.
:returns: xml string
"""
# load some useful actions so we don't have to fetch them repeatedly
resource_show = toolkit.get_action('resource_show')
package_show = toolkit.get_action('package_show')
# get the resources and packages associated with the query
resources = [resource_show({}, {'id': r}) for r in self._query.resource_ids]
packages = [package_show({}, {'id': r['package_id']}) for r in resources]
# useful bools
single_resource = len(resources) == 1
single_package = len(packages) == 1
empty_query = self._query.query == {}
# define some site variables
site_org = {
'organizationName': utils.get_setting(
'ckanext.versioned_datastore.dwc_org_name',
'ckanext.doi.publisher',
'ckan.site_title',
),
'electronicMailAddress': utils.get_setting(
'ckanext.versioned_datastore.dwc_org_email', 'smtp.mail_from'
),
'onlineUrl': utils.get_setting('ckan.site_url'),
}
site_name = utils.get_setting('ckanext.doi.site_title', 'ckan.site_title')
site_url = utils.get_setting('ckan.site_url', default='')
# get the license
licenses = list(
set(
[
p.get('license_title')
for p in packages
if p.get('license_title') is not None
]
)
)
query_license = (
licenses[0]
if len(licenses) == 1
else utils.get_setting(
'ckanext.versioned_datastore.dwc_default_license', default='null'
)
)
# generate a string representing the records' location, e.g. a single resource
# name, a package name, or the whole site
if single_resource:
container_name = resources[0]['name']
elif single_package:
container_name = f'{len(resources)} resources in {packages[0]["title"]}'
else:
container_name = site_name
# generate title and abstract
query_title = self._eml_title or f'Query on {container_name}'
query_abstract = (
self._eml_abstract
or f'Query ID {self._query.hash} on {container_name} ({self.rows_written} records).'
)
# set up the metadata dict in order (otherwise GBIF complains) with some defaults
dataset_metadata = OrderedDict(
{
'alternateIdentifier': [self._query.hash],
'title': query_title,
'creator': [site_org],
'metadataProvider': [site_org],
'pubDate': dt.now().strftime('%Y-%m-%d'),
'language': utils.get_setting('ckan.locale_default'),
'abstract': {'para': query_abstract},
'keywordSet': [],
'intellectualRights': {'para': query_license},
'distribution': (
{'online': {'url': (site_url, {'function': 'information'})}},
{'scope': 'document'},
),
'coverage': {
'geographicCoverage': {
'geographicDescription': 'Unbound',
'boundingCoordinates': {
'westBoundingCoordinate': -180,
'eastBoundingCoordinate': 180,
'northBoundingCoordinate': -90,
'southBoundingCoordinate': 90,
},
}
},
'contact': [site_org],
}
)
additional_metadata = {
'metadata': {
'gbif': {
'dateStamp': dt.now().strftime('%Y-%m-%dT%H:%M:%SZ'),
'citation': None,
'resourceLogoUrl': site_url
+ toolkit.config.get('ckan.site_logo', ''),
}
}
}
if single_package and empty_query:
# all the resources are in a single package (even if not all resources in
# that package are included), so link to the package
dataset_metadata['distribution'][0]['online']['url'] = (
toolkit.url_for('dataset.read', id=packages[0]['id'], qualified=True),
{'function': 'information'},
)
# also link to the package via the doi
if 'doi' in packages[0]:
dataset_metadata['alternateIdentifier'].append(
'doi:' + packages[0]['doi']
)
pkg_year = toolkit.h.package_get_year(packages[0])
pkg_title = packages[0]['title']
pkg_doi = packages[0]['doi']
pkg_author = packages[0]['author']
additional_metadata['metadata']['gbif']['citation'] = (
f'{pkg_author} ({pkg_year}). Dataset: {pkg_title}. {site_name}',
{'identifier': f'https://doi.org/{pkg_doi}'},
)
if single_resource and empty_query:
# if it's just downloading one resource with no filters, we can be even
# more specific with some of the metadata
resource = resources[0]
package = packages[0]
dataset_metadata['title'] = resource['name']
dataset_metadata['alternateIdentifier'] += [resource['id']]
dataset_metadata['pubDate'] = package.get(
'metadata_modified', resource.get('created')
)
dataset_metadata['abstract']['para'] = resource.get('description')
dataset_metadata['distribution'][0]['online']['url'] = (
toolkit.url_for(
'resource.read',
id=package['id'],
resource_id=resource['id'],
qualified=True,
),
{'function': 'information'},
)
elif plugin_loaded('query_dois'):
from ckanext.query_dois.lib.doi import find_existing_doi
from ckanext.query_dois.lib.query import Query
query_doi = find_existing_doi(
Query.create(
self._query.resource_ids,
self._query.version,
self._query.query,
self._query.query_version,
)
)
if query_doi:
dataset_metadata['alternateIdentifier'] += ['doi:' + query_doi.doi]
dataset_metadata['distribution'][0]['online']['url'] = (
toolkit.url_for(
'query_doi.landing_page',
data_centre=utils.get_setting('ckanext.query_dois.prefix'),
identifier=query_doi.doi.split('/', 1)[-1],
qualified=True,
),
{'function': 'information'},
)
additional_metadata['metadata']['gbif']['citation'] = (
toolkit.h.create_multisearch_citation_text(query_doi, html=False),
{'identifier': f'https://doi.org/{query_doi.doi}'},
)
if (
self.schema.core_extension
and self.schema.core_extension.location.base == urls.GBIFUrls.base_url
):
dataset_metadata['keywordSet'].append(
{
'keyword': self.schema.row_type_name,
'keywordThesaurus': f'GBIF Dataset Type Vocabulary: {urls.GBIFUrls.thesaurus}',
}
)
if plugin_loaded('attribution'):
package_contributions_show = toolkit.get_action(
'package_contributions_show'
)
authors = []
for r in resources:
contributions = package_contributions_show({}, {'id': r['package_id']})
for c in contributions['contributions']:
if c['agent']['id'] in authors:
continue
agent = {}
if c['agent']['external_id']:
agent['userId'] = (
c['agent']['external_id'],
{'directory': c['agent']['external_id_url']},
)
if c['agent']['agent_type'] == 'person':
agent['individualName'] = {
'givenName': c['agent']['given_names'],
'surName': c['agent']['family_name'],
}
else:
agent['organizationName'] = c['agent']['name']
dataset_metadata['creator'].append(agent)
authors.append(c['agent']['id'])
for plugin in idownload_implementations():
dataset_metadata = plugin.download_modify_eml(dataset_metadata, self._query)
nsmap = utils.NSMap(
eml=urls.XMLUrls.eml,
dc=urls.XMLUrls.dc,
xsi=urls.XMLUrls.xsi,
xml=urls.XMLUrls.xml,
)
root = etree.Element(
nsmap.ns('eml', 'eml'),
nsmap=nsmap,
attrib={
'scope': 'system',
'system': 'http://gbif.org',
nsmap.ns('xsi', 'schemaLocation'): ' '.join(
[urls.XMLUrls.eml, urls.GBIFUrls.eml]
),
'packageId': self.output_name,
nsmap.ns('xml', 'lang'): 'en',
},
)
for i in utils.json_to_xml('dataset', dataset_metadata):
root.append(i)
if additional_metadata['metadata']['gbif'].get('citation') is not None:
for i in utils.json_to_xml('additionalMetadata', additional_metadata):
root.append(i)
return etree.tostring(root, pretty_print=True).decode()
|