Modules

names: Parse scientific names.
source: Describe a source dataset.
sourceio: Read and write sources and source properties.
taxamatch: Match scientific names.
types

Constants

LICENSES : Object

Common data licenses.

Each property is a license identifier. The value is an object with the following properties:

spdx: Whether the license is in the Software Package Data Exchange (SPDX) license list.
name: License name.
url: License URL.

Functions

downloadFile(url, dir) ⇒ object | null

Download file and compute MD5 hash of the stream.

loadPage(url, page) ⇒ Promise.<puppeteer.HTTPResponse>

Load URL in browser page.

readPageHtml(page) ⇒ Promise.<string>

Read browser page as HTML.

readPageMhtml(page) ⇒ Promise.<string>

Read browser page as MHTML.

readPagePng(page) ⇒ Promise.<Buffer>

Read browser page as PNG.

readPagePdf(page) ⇒ Promise.<Buffer>

Read browser page as PDF.

md5(x) ⇒ string

Compute MD5 hash.

hashFile(file) ⇒ Promise.<string>

Compute MD5 hash of a file read as a stream.

Uses base64 encoding by default as it was found to be much faster for large binary files and same as UTF-8 for text.

buildPath(url, checksum, date) ⇒ string

Build archive path.

log(params) ⇒ Promise.<ArchiveEntry>

Add an entry to the archive log.

guessFilename(headers, defaultBasename, url) ⇒ string

Guess filename from HTTP response headers.

logData(params) ⇒ ArchiveEntry

Write data to file and add to log.

search(params, options) ⇒ Array.<ArchiveEntry>

Search log for matching entries.

getBrowser() ⇒ Promise.<puppeteer.Browser>

Get cached browser instance.

downloadFile(params) ⇒ Promise.<ArchiveEntry>

Download file from URL and log result.

downloadArcgisFeatureLayer(params) ⇒ Promise.<ArchiveEntry>

Download features from ArcGIS Feature Layer and log result.

registerFile(params) ⇒ Promise.<ArchiveEntry>

Register existing file in archive log.

buildWfsDownloadUrl(url) ⇒ object

Build WFS GetFeature URL.

downloadPage(params) ⇒ Promise.<ArchiveEntry>

Download web page as MHTML and log result.

Page is rendered in a headless browser (puppeteer) and saved as MHTML.

geocode(address) ⇒ Promise.<object>

Geocode address.

geocodeCached(address) ⇒ Promise.<object>

Geocode address with caching.

buildGetCapabilitiesUrl(url) ⇒ string

Build WFS GetCapabilities URL.

parseCapabilities(xml) ⇒ object

Parse WFS GetCapabilities response.

chooseOutputFormat(formats) ⇒ string | null

Choose the output format.

buildGetFeatureUrl(url, capabilities, paging) ⇒ string

Build WFS GetFeature URL.

names

Parse scientific names.

names
- ~ScientificName
  - new ScientificName(obj)
  - instance
    - .toString(options) ⇒ string
    - .warnings() ⇒ Array.<string>
    - .errors() ⇒ Array.<string>
    - .report() ⇒ object
  - static
    - .fromString(str) ⇒ ScientificName
    - .fromFields(fields) ⇒ ScientificName
    - .compareStrings(options) ⇒ function
- ~GENERIC
- ~SPECIFIC
- ~SUBG
- ~SP
- ~RANKS
- ~RANK
- ~HEAD
- ~UNINOMIAL
- ~GENUS
- ~HYBRID_GENUS
- ~SUBGENUS
- ~SPECIES
- ~INFRASPECIES
- ~RANK_EPITHET
- ~CULTIVAR
- ~FIRST
- ~HYBRID
- ~cleanName(s) ⇒ string
- ~parseInfraspecies(s) ⇒ Array.<Infraspecies>
- ~printInfraspecies(infraspecies, options) ⇒ string
- ~printScientificName(name, [options]) ⇒ string
- ~formatScientificName(name, defaultGenus) ⇒ ParsedScientificName
- ~parseScientificName(name) ⇒ ParsedScientificName

names~ScientificName

Class representing a scientific name.

Kind: inner class of names
Properties

Name	Type	Description
parsed	`ParsedScientificName`	Parsed scientific name.
[input]	`string` \| `object`	Input from which `parsed` was derived.
[matches]	`Array.<object>`	Matches from a taxonomic database.

~ScientificName
- new ScientificName(obj)
- instance
  - .toString(options) ⇒ string
  - .warnings() ⇒ Array.<string>
  - .errors() ⇒ Array.<string>
  - .report() ⇒ object
- static
  - .fromString(str) ⇒ ScientificName
  - .fromFields(fields) ⇒ ScientificName
  - .compareStrings(options) ⇒ function

new ScientificName(obj)

Param	Type	Description
obj	`ParsedScientificName`	Parsed scientific name.

scientificName.toString(options) ⇒ `string`

Print scientific name to string.

Kind: instance method of ScientificName

Param	Type	Description
options	`object`	Print options (see printScientificName).

Example

ScientificName.fromString(`Malus pumila var. asiatica 'Gala'`).toString()
// "Malus pumila var. asiatica 'Gala'"

scientificName.warnings() ⇒ `Array.<string>`

Get warnings.

Kind: instance method of ScientificName
Example

ScientificName.fromString('... Malus x pumila ...').warnings()
// [ 'Unparsed head', 'Unparsed tail', 'Hybrid' ]
ScientificName.fromFields({genus: 'Malus', species: 'pumila', scientific: 'Pyrus communis'}).warnings()
// [ 'Inconsistent secondary fields: genus, species' ]

scientificName.errors() ⇒ `Array.<string>`

Get errors.

Kind: instance method of ScientificName
Example

(new ScientificName({species: 'pumila'})).errors()
// [ 'Missing genus' ]

scientificName.report() ⇒ `object`

Get full report.

Kind: instance method of ScientificName
Example

ScientificName.fromString('... Malus x pumila ...').report()
// {
//    input: '... Malus x pumila ...',
//    parsed: {
//      head: '... ',
//      genus: 'Malus',
//      species: 'pumila',
//      hybrid: true,
//      tail: '...'
//    },
//    warnings: [ 'Unparsed head', 'Unparsed tail', 'Hybrid' ]
// }

ScientificName.fromString(str) ⇒ `ScientificName`

Build scientific name from string.

Kind: static method of ScientificName

Param	Type
str	`string`

Example

ScientificName.fromString('Malus pumila')
// ScientificName {
//   parsed: { genus: 'Malus', species: 'pumila' },
//   input: 'Malus pumila'
// }

ScientificName.fromFields(fields) ⇒ `ScientificName`

Build scientific name from feature fields.

Kind: static method of ScientificName

Param	Type
fields	`object`

Example

ScientificName.fromFields({ scientific: 'Malus pumila', other: 'Bloop' })
// ScientificName {
//   parsed: { genus: 'Malus', species: 'pumila' },
//   input: { scientific: 'Malus pumila' }
// }
ScientificName.fromFields({ genus: 'malus', species: 'PLATANOÏDES' })
// ScientificName {
//   parsed: { genus: 'Malus', species: 'platanoides' },
//   input: { genus: 'malus', species: 'PLATANOÏDES'}
// }

ScientificName.compareStrings(options) ⇒ `function`

Generate compare function for sorting by string representation.

Kind: static method of ScientificName
Returns: function - Compare function (a, b).

Param	Type	Description
options	`object`	Print options (see printScientificName).

Example

l = [new ScientificName({genus: 'Prunus'}), new ScientificName({genus: 'Malus'})]
l.sort(ScientificName.compareStrings())
// [
//   ScientificName { parsed: { genus: 'Malus' } },
//   ScientificName { parsed: { genus: 'Prunus' } }
// ]