YASMEEN input data parser

"Yet Another Species Matching Execution ENgine" - Input data parser CLI tool

Purposes

The YASMEEN Input data parser is the command line (CLI) tool that implements the first step in the YASMEEN data flow.

It ingests, pre-processes, parses, post-processes and converts in the proper format, a set of input data provided as unstructured (or semi-structured) lines in a text file.

Command line

java -jar YASMINE-parser-<version>.jar <options>

You can launch it with the '-h' option to get a report of the available options with their description:

java -jar YASMINE-parser-<version>.jar -h

Will give:

usage: InputDataParser:
 -dataSourceId <arg>             Specify the identifier for the data source originating the input data. Defaults to
                                 'UserProvidedData' when not set
 -h                              Print this message
 -inFile <arg>                   Specify a path to the file containing unstructured input data (one per line)
 -noHeader                       Omit the CSV header in the produced parsed results file
 -outFile <arg>                  Specify a path to the file that will contain the structured parsed results
 -parser <arg>                   Specify one of the available input parsers among { GNI (Global Names Index), 
                                 IDENTITY (No action), SIMPLE (Simple, regexp-based) }
 -postParsingRuleset <arg>       Specify an embedded post-parsing ruleset among { bionymPostparsingRules }
 -postParsingRulesetFile <arg>   Specify a file containing a post-parsing ruleset
 -preParsingRuleset <arg>        Specify an embedded pre-parsing ruleset among { commonPreparsingRules, otherPreparsingRules,
                                 bionymPreparsingRules }
 -preParsingRulesetFile <arg>    Specify a file containing a pre-parsing ruleset

Command line options

-h

This option requires no arguments, and - when enabled - will print the help message and exit (no parsing will be performed)

-inFile

Mandatory.

Specifies the path to a file containing unstructured (or semi-structured) input data, one per line.

-outFile

Optional.

Specifies the path of the output file. When not specified, the output will be written in a file with the same name of the input file with '.parsed' appended.

-noHeader

Optional.

This option requires no arguments, and - when enabled - will produce an output file with no header row.

preParsingRuleset

Optional.

Selects one of the embedded pre-parsing rulesets that will be applied to the input data. Pre-processed input data (according to the selected ruleset) will then be sent to the selected parser for processing. If no pre-processing ruleset is specified, then the input data will be parsed as is.

This option can be specified multiple times. Currently available embedded pre-parsing rulesets are:

• commonPreParsingRuleset: removes leading / trailing spaces and collapses multiple spaces into single spaces.
• otherPreParsingRuleset: performs substitution of common patterns appearing in the input data to improve parser's efficacy.
• bionymPreParsingRuleset: performs additional substitution of patterns appearing in the input data to improve parser's efficacy. Includes rules as Uncertain identification, Drop subspecies indication, Standardise variety indication and Standardise form indication originally appearing in Edward Vanden Berghe bionym.R script.

-parser

Mandatory.

Selects which of the available input parsers will be used to extract (or attempt to extract) scientific name and authorship information from the raw input data.

Currently available parsers are:

• SIMPLE: a simple, regexp-based embedded parser. Works well in most cases and is reasonably fast. Accepts unstructured inputs.
• GNI: an external, remote parser maintained by Mr. Dimitri Mozzherin (at gni.org). Very accurate, grammar-based, albeit possibly slow due to network latency. tRequires a working internet connection on the host machine executing the parser tool. Accepts unstructured inputs.
• IDENTITY: a simple, embedded parser that doesn't perform any parsing at all. It accepts semi-structured inputs (input file lines must be in the form <scientific name>;<author>) and simply provides the two parts separately.