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DwC-A localities: include remaining now_loc fields

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This commit is contained in:
karilint
2026-04-28 10:38:21 +03:00
parent 101fac67b7
commit 30040eaeeb
2 changed files with 322 additions and 1 deletions
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backend/src/services/dwcArchiveExportLocalities.ts
+295 -1
View File
@@ -130,6 +130,7 @@ type LocalityForExport = Pick<
| 'dec_long'
| 'dms_lat'
| 'dms_long'
| 'approx_coord'
| 'altitude'
| 'loc_detail'
| 'chron'
@@ -148,6 +149,8 @@ type LocalityForExport = Pick<
| 'date_meth'
| 'age_comm'
| 'site_area'
| 'gen_loc'
| 'plate'
| 'appr_num_spm'
| 'num_spm'
| 'true_quant'
@@ -176,6 +179,12 @@ type LocalityForExport = Pick<
| 'invert_pres'
| 'time_rep'
| 'taph_comm'
| 'tax_comm'
| 'datum_plane'
| 'tos'
| 'bos'
| 'loc_status'
| 'hominin_skeletal_remains'
| 'climate_type'
| 'biome'
| 'v_ht'
@@ -214,6 +223,29 @@ type LocalityForExport = Pick<
now_syn_loc: ReadonlyArray<{ synonym: string | null }>
now_ss: ReadonlyArray<{ sed_struct: string }>
now_coll_meth: ReadonlyArray<{ coll_meth: string }>
now_mus: ReadonlyArray<{
museum: string
com_mlist: {
institution: string
alt_int_name: string | null
city: string | null
state: string | null
country: string | null
}
}>
now_plr: ReadonlyArray<{
now_proj: {
proj_code: string | null
proj_name: string | null
proj_status: string | null
}
}>
now_lau: ReadonlyArray<{
lau_date: Date | null
lau_comment: string | null
com_people_now_lau_lau_coordinatorTocom_people: { full_name: string }
com_people_now_lau_lau_authorizerTocom_people: { full_name: string }
}>
now_ls: ReadonlyArray<{
com_species: {
order_name: string
@@ -263,7 +295,11 @@ export const mapLocalityToLocationRow = (locality: LocalityForExport): LocationC
verbatimLatitude: toMaybeMeaningful(locality.dms_lat),
verbatimLongitude: toMaybeMeaningful(locality.dms_long),
verbatimElevation: locality.altitude === null || locality.altitude === undefined ? '' : String(locality.altitude),
locationRemarks: [toMaybeMeaningful(locality.loc_detail), toMaybeMeaningful(locality.age_comm)]
locationRemarks: [
toMaybeMeaningful(locality.loc_detail),
toMaybeMeaningful(locality.age_comm),
toMaybeMeaningful(locality.tax_comm),
]
.filter(Boolean)
.join(' | '),
}
@@ -451,6 +487,27 @@ const LOCALITY_MEASUREMENT_MAPPINGS: Array<{
// TODO(#1150): Add unit and definition for NOW locality site_area.
measurementMethod: '',
},
{
field: 'approx_coord',
measurementType: 'approximate coordinates',
measurementUnit: '',
// TODO(#1150): Add definition (what qualifies as approximate).
measurementMethod: '',
},
{
field: 'gen_loc',
measurementType: 'general locality',
measurementUnit: '',
// TODO(#1150): Add controlled vocabulary / definition.
measurementMethod: '',
},
{
field: 'plate',
measurementType: 'tectonic plate',
measurementUnit: '',
// TODO(#1150): Add controlled vocabulary / definition.
measurementMethod: '',
},
{
field: 'appr_num_spm',
measurementType: 'approximate number of specimens',
@@ -584,6 +641,20 @@ const LOCALITY_MEASUREMENT_MAPPINGS: Array<{
// TODO(#1150): Add field description.
measurementMethod: '',
},
{
field: 'loc_status',
measurementType: 'locality status',
measurementUnit: '',
// TODO(#1150): Add definition.
measurementMethod: '',
},
{
field: 'hominin_skeletal_remains',
measurementType: 'Hominin skeletal remains (field)',
measurementUnit: '',
// TODO(#1150): Add field description.
measurementMethod: '',
},
{
field: 'assem_fm',
measurementType: 'Assemblage Formation',
@@ -875,6 +946,13 @@ export const mapLocalityToMeasurementRows = (locality: LocalityForExport): Local
const maxAgeId = buildLocalityMeasurementId(lid, 'max_age')
const minAgeId = buildLocalityMeasurementId(lid, 'min_age')
const stratigraphyParentId = buildLocalityMeasurementId(lid, 'stratigraphy')
const tosId = buildLocalityMeasurementId(lid, 'tos')
const bosId = buildLocalityMeasurementId(lid, 'bos')
const datumPlaneId = buildLocalityMeasurementId(lid, 'datum_plane')
const lastUpdateParentId = buildLocalityMeasurementId(lid, 'last_update')
const hasMaxAgeGroup =
isMeaningfulMeasurementValue(locality.max_age) ||
isMeaningfulMeasurementValue(locality.bfa_max) ||
@@ -891,6 +969,135 @@ export const mapLocalityToMeasurementRows = (locality: LocalityForExport): Local
const rows: LocalityMeasurementCsvRow[] = []
const hasAnyStratigraphy =
isMeaningfulMeasurementValue(locality.datum_plane) ||
isMeaningfulMeasurementValue(locality.tos) ||
isMeaningfulMeasurementValue(locality.bos)
if (hasAnyStratigraphy) {
rows.push({
taxonID,
measurementID: stratigraphyParentId,
parentMeasurementID: '',
measurementType: 'stratigraphic section',
verbatimMeasurementType: 'stratigraphy',
measurementValue: '',
measurementUnit: '',
// TODO(#1150): Add field description.
measurementMethod: '',
})
}
if (isMeaningfulMeasurementValue(locality.datum_plane)) {
rows.push({
taxonID,
measurementID: datumPlaneId,
parentMeasurementID: hasAnyStratigraphy ? stratigraphyParentId : '',
measurementType: 'datum plane',
verbatimMeasurementType: 'datum_plane',
measurementValue: toMaybeMeaningful(locality.datum_plane),
measurementUnit: '',
// TODO(#1150): Add field description.
measurementMethod: '',
})
}
if (typeof locality.tos === 'number') {
const value = toMaybeMeaningfulNumberWithZeroOption(locality.tos, { allowZero: true })
if (value) {
rows.push({
taxonID,
measurementID: tosId,
parentMeasurementID: hasAnyStratigraphy ? stratigraphyParentId : '',
measurementType: 'top of section',
verbatimMeasurementType: 'tos',
measurementValue: value,
measurementUnit: '',
// TODO(#1150): Add unit and definition.
measurementMethod: '',
})
}
}
if (typeof locality.bos === 'number') {
const value = toMaybeMeaningfulNumberWithZeroOption(locality.bos, { allowZero: true })
if (value) {
rows.push({
taxonID,
measurementID: bosId,
parentMeasurementID: hasAnyStratigraphy ? stratigraphyParentId : '',
measurementType: 'bottom of section',
verbatimMeasurementType: 'bos',
measurementValue: value,
measurementUnit: '',
// TODO(#1150): Add unit and definition.
measurementMethod: '',
})
}
}
const lastUpdate = locality.now_lau[0]
if (lastUpdate) {
rows.push({
taxonID,
measurementID: lastUpdateParentId,
parentMeasurementID: '',
measurementType: 'last update',
verbatimMeasurementType: 'now_lau',
measurementValue: '',
measurementUnit: '',
measurementMethod: '',
})
if (lastUpdate.lau_date) {
rows.push({
taxonID,
measurementID: buildLocalityMeasurementId(lid, 'last_update_date'),
parentMeasurementID: lastUpdateParentId,
measurementType: 'last update date',
verbatimMeasurementType: 'now_lau.lau_date',
measurementValue: lastUpdate.lau_date.toISOString().slice(0, 10),
measurementUnit: '',
measurementMethod: '',
})
}
rows.push({
taxonID,
measurementID: buildLocalityMeasurementId(lid, 'last_update_coordinator'),
parentMeasurementID: lastUpdateParentId,
measurementType: 'last update coordinator',
verbatimMeasurementType: 'now_lau.lau_coordinator',
measurementValue: toMaybeMeaningful(lastUpdate.com_people_now_lau_lau_coordinatorTocom_people.full_name),
measurementUnit: '',
measurementMethod: '',
})
rows.push({
taxonID,
measurementID: buildLocalityMeasurementId(lid, 'last_update_authorizer'),
parentMeasurementID: lastUpdateParentId,
measurementType: 'last update authorizer',
verbatimMeasurementType: 'now_lau.lau_authorizer',
measurementValue: toMaybeMeaningful(lastUpdate.com_people_now_lau_lau_authorizerTocom_people.full_name),
measurementUnit: '',
measurementMethod: '',
})
if (isMeaningfulString(lastUpdate.lau_comment)) {
rows.push({
taxonID,
measurementID: buildLocalityMeasurementId(lid, 'last_update_comment'),
parentMeasurementID: lastUpdateParentId,
measurementType: 'last update comment',
verbatimMeasurementType: 'now_lau.lau_comment',
measurementValue: lastUpdate.lau_comment.trim(),
measurementUnit: '',
measurementMethod: '',
})
}
}
if (hasAnyAgeBasis) {
rows.push({
taxonID,
@@ -978,6 +1185,63 @@ export const mapLocalityToMeasurementRows = (locality: LocalityForExport): Local
rows.push(...coreRows)
const museums = locality.now_mus
.map(row => {
const institution = row.com_mlist.alt_int_name ?? row.com_mlist.institution
const locationBits = [
toMaybeMeaningful(row.com_mlist.city),
toMaybeMeaningful(row.com_mlist.state),
toMaybeMeaningful(row.com_mlist.country),
]
.filter(Boolean)
.join(', ')
return [row.museum, institution, locationBits ? `(${locationBits})` : ''].filter(Boolean).join(' ')
})
.filter(isMeaningfulString)
.map(value => value.trim())
if (museums.length) {
rows.push({
taxonID,
measurementID: buildLocalityMeasurementId(lid, 'museums'),
parentMeasurementID: '',
measurementType: 'Museums',
verbatimMeasurementType: 'now_mus.museum',
measurementValue: museums.join('|'),
measurementUnit: '',
// TODO(#1150): Add field description.
measurementMethod: '',
})
}
const projects = locality.now_plr
.map(row => row.now_proj)
.map(project =>
[
toMaybeMeaningful(project.proj_code),
toMaybeMeaningful(project.proj_name),
toMaybeMeaningful(project.proj_status),
]
.filter(Boolean)
.join(' - ')
)
.filter(isMeaningfulString)
.map(value => value.trim())
if (projects.length) {
rows.push({
taxonID,
measurementID: buildLocalityMeasurementId(lid, 'projects'),
parentMeasurementID: '',
measurementType: 'Projects',
verbatimMeasurementType: 'now_plr.pid',
measurementValue: projects.join('|'),
measurementUnit: '',
// TODO(#1150): Add field description.
measurementMethod: '',
})
}
const collectingMethods = locality.now_coll_meth
.map(method => method.coll_meth)
.filter(value => isMeaningfulString(value))
@@ -1227,6 +1491,7 @@ export const buildDwcLocalityArchiveZipBuffer = async (): Promise<Buffer> => {
dec_long: true,
dms_lat: true,
dms_long: true,
approx_coord: true,
altitude: true,
loc_detail: true,
chron: true,
@@ -1245,6 +1510,8 @@ export const buildDwcLocalityArchiveZipBuffer = async (): Promise<Buffer> => {
date_meth: true,
age_comm: true,
site_area: true,
gen_loc: true,
plate: true,
appr_num_spm: true,
num_spm: true,
true_quant: true,
@@ -1273,6 +1540,12 @@ export const buildDwcLocalityArchiveZipBuffer = async (): Promise<Buffer> => {
invert_pres: true,
time_rep: true,
taph_comm: true,
tax_comm: true,
datum_plane: true,
tos: true,
bos: true,
loc_status: true,
hominin_skeletal_remains: true,
climate_type: true,
biome: true,
v_ht: true,
@@ -1320,6 +1593,27 @@ export const buildDwcLocalityArchiveZipBuffer = async (): Promise<Buffer> => {
now_coll_meth: {
select: { coll_meth: true },
},
now_mus: {
select: {
museum: true,
com_mlist: { select: { institution: true, alt_int_name: true, city: true, state: true, country: true } },
},
},
now_plr: {
select: {
now_proj: { select: { proj_code: true, proj_name: true, proj_status: true } },
},
},
now_lau: {
take: 1,
orderBy: { lau_date: 'desc' },
select: {
lau_date: true,
lau_comment: true,
com_people_now_lau_lau_coordinatorTocom_people: { select: { full_name: true } },
com_people_now_lau_lau_authorizerTocom_people: { select: { full_name: true } },
},
},
now_ls: {
select: {
com_species: {
backend/src/unit-tests/dwcArchiveExportLocalities.test.ts
+27
View File
@@ -21,6 +21,7 @@ describe('DwC-A locality export mapping', () => {
dec_long: 24.9384,
dms_lat: null,
dms_long: null,
approx_coord: null,
altitude: 123,
loc_detail: 'Some notes',
chron: 'Test chron',
@@ -39,6 +40,8 @@ describe('DwC-A locality export mapping', () => {
date_meth: 'radioisotope',
age_comm: 'Age comment',
site_area: null,
gen_loc: null,
plate: null,
appr_num_spm: null,
num_spm: null,
true_quant: null,
@@ -67,6 +70,12 @@ describe('DwC-A locality export mapping', () => {
invert_pres: null,
time_rep: null,
taph_comm: null,
tax_comm: null,
datum_plane: null,
tos: null,
bos: null,
loc_status: null,
hominin_skeletal_remains: false,
climate_type: null,
biome: null,
v_ht: null,
@@ -102,6 +111,9 @@ describe('DwC-A locality export mapping', () => {
now_syn_loc: [],
now_ss: [],
now_coll_meth: [],
now_mus: [],
now_plr: [],
now_lau: [],
now_ls: [],
now_time_unit_now_loc_bfa_maxTonow_time_unit: null,
now_time_unit_now_loc_bfa_minTonow_time_unit: null,
@@ -155,6 +167,21 @@ describe('DwC-A locality export mapping', () => {
expect(collectingMethodsRow?.measurementValue).toEqual('screenwash|quarry')
})
it('uses parentMeasurementID for stratigraphy fields', () => {
const rows = mapLocalityToMeasurementRows({
...baseLocality,
datum_plane: 'Datum',
tos: 0,
bos: 12.5,
})
const parent = rows.find(r => r.verbatimMeasurementType === 'stratigraphy')
expect(parent).toBeTruthy()
const tosRow = rows.find(r => r.verbatimMeasurementType === 'tos')
const bosRow = rows.find(r => r.verbatimMeasurementType === 'bos')
expect(tosRow?.parentMeasurementID).toEqual(parent?.measurementID)
expect(bosRow?.parentMeasurementID).toEqual(parent?.measurementID)
})
it('generates a ZIP archive with expected files', async () => {
const zipBuffer = await buildDwcLocalityArchiveZipBufferFromLocalities([baseLocality])
const zip = await JSZip.loadAsync(zipBuffer)