View source for 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 [[YASMEEN#PARSE_INPUT_DATA|PARSE INPUT DATA]] step in the YASMEEN [[YASMEEN#Data_flow|data flow]].

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

== Command line ==

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

This CLI tool can be launched with the '-h' option to get a report of the available options:

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

Will give:

 usage:
  -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

=== General command line options ===
==== -h ====

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

=== Input file command line options ===
==== -inFile ====

Mandatory. 

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

=== Pre-parsing command line options ===
==== -preParsingRuleset ====

Optional.

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

This option can be specified multiple times and selected rule sets will be applied in the same order as they're specified on the command line. Please note that rule set ordering '''DOES''' matter. 

Currently available embedded pre-parsing rule sets are:

===== '''''otherPreparsingRules''''' ===== 

Performs substitution of common patterns appearing in the input data to improve parser's efficacy (see the actual ruleset [[#otherPreparsingRules_definition|definition]]).

===== '''''bionymPreParsingRules''''' =====

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 (see the actual ruleset [[#bionymPreparsingRules_definition|definition]]).

===== '''''commonPreParsingRules''''' =====

Removes leading / trailing spaces and collapses multiple spaces into single spaces (see the actual ruleset [[#commonPreparsingRules_definition|definition]]).

==== -preParsingRulesetFile ====

Optional.

Specifies an external pre-parsing ruleset file that will be applied to the input data. Pre-parsedinput data (according to the selected ruleset) will then be sent to the selected parser for processing. If no pre-processing ruleset file is specified, then the input data will be sent to the parser as it is.

This option can be specified multiple times.

=== Parser command line options ===
==== -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:

===== '''GNI''' ===== 
A wrapper to an external, remote parser maintained by Dimitri Mozzherin (at [http://www.globalnames.org/ www.globalnames.org]). Very accurate, grammar-based, albeit possibly slow due to network latency: requires a working internet connection on the host machine executing the parser tool, as it needs to contact the GNI remote parser to get the actual results. Accepts unstructured inputs.

The GNI remote parser can be queried via URLs like:

 http://gni.globalnames.org/parsers.xml?names=Membranophtera+spinulosa+(Ruprecht)Küntze+1891

===== '''SIMPLE''' ===== 
A simple, regexp-based embedded parser. Works well in most cases and is reasonably fast (as it is executed locally). Accepts unstructured inputs.

===== '''IDENTITY''' ===== 
A simple, embedded parser that doesn't perform any parsing at all. It accepts [[YASMEEN_data_formats#Example_of_semi-structured_input_data|semi-structured]] inputs (input file lines must be in the form <scientific name>;<author>) and simply provides the two parts separately.

=== Post-parsing command line options ===
==== -postParsingRuleset ====

Optional.

Selects one of the embedded post-parsing rulesets that will be applied to the parsed input data. If no post-parsing ruleset is specified, then the parsed input data will remain as they are.

This option can be specified multiple times and selected rule sets will be applied in the same order as they're specified on the command line. Please note that rule set ordering '''DOES''' matter. 

Currently available embedded post-parsing rule sets are:

===== '''''bionymPostparsingRules''''' =====

Performs additional substitution of patterns appearing in the parsed scientific name. Includes rules as ''Remove temporary species indication'' originally appearing in Edward Vanden Berghe ''bionym.R'' script (see the actual ruleset [[#bionymPostparsingRules_definition|definition]]).

==== -postParsingRulesetFile ====

Optional.

Specifies an external post-parsing ruleset file that will be applied to the parsed input data. If no post-processing ruleset file is specified, then the parsed input data will remain as they are.

This option can be specified multiple times.

=== Output file command line options ===
==== -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.

== Usage examples ==

=== Simple invocation (no pre-parsing, no post-parsing) ===

* Parse unstructured input file 'input.txt' with the SIMPLE parser, emitting parsed results in 'input.out', without applying any pre-parsing or post-parsing ruleset:

 java -jar YASMEEN-parser-<version>.jar -inFile input.txt -outFile input.out -parser SIMPLE

=== Invocation with embedded pre-parsing rulesets only ===

* Parse unstructured input file 'input.txt' with the GNI parser, emitting parsed results in 'input.out', applying the embedded pre-parsing rulesets 'commonPreparsingRules' and 'bionymPreparsingRules' and no post-parsing ruleset:

 java -jar YASMEEN-parser-<version>.jar -inFile input.txt -outFile input.out -parser GNI -preParsingRuleset commonPreparsingRules -preParsingRuleset bionymPreparsingRules 

=== Invocation with embedded and external pre-parsing and post-parsing rulesets ===
 
* Parse unstructured input file 'input.txt' with the GNI parser, emitting parsed results in 'input.out', applying the embedded pre-parsing ruleset 'commonPreparsingRules', an external pre-parsing ruleset in ./pre/myOwnPreparsingRules.xml, the embedded post-parsing ruleset 'bionymPostparsingRules' and an external post-parsing ruleset in ./post/myOwnPostparsingRules.xml:

 java -jar YASMEEN-parser-<version>.jar -inFile input.txt -outFile input.out -parser GNI -preParsingRuleset commonPreparsingRules -preParsingRulesetFile ./pre/myOwnPreparsingRules.xml -postParsingRuleset bionymPostparsingRules 
 -postParsingRulesetFile ./post/myOwnPostparsingRules.xml

== Appendix ==

=== Pre-parsing rules ===

Pre-parsing rules will transform the raw input data ''''before''''' it is sent to the parser.

These rules are modeled as simple pairs of RegEx patterns and replacements. The RegEx syntax is exactly the same as that available in Java 6. See: [http://docs.oracle.com/javase/6/docs/api/java/util/regex/Pattern.html Pattern javadoc] and [http://docs.oracle.com/javase/6/docs/api/java/util/regex/Matcher.html Matcher javadoc].

An example of (dummy) pre-parsing rule is:

 <PreparsingRule id="foo">
        <Description>Dummy regexp</Description>
        <Match>(a|e|i|o|u|y)</Match>
        <Transform>$1x</Transform>
 </PreparsingRule>

This example rule will append a literal 'x' to all vowels appearing in the input data. 

Note the '$' character appearing in the <Transform/> element (the replacement): it is used to reference - in the replacement - the first ($1) group captured by the RegEx in the <Match/> element.

Special escaping is needed when literal '$' and '\' must appear in the replacement (see the [http://docs.oracle.com/javase/6/docs/api/java/util/regex/Matcher.html#quoteReplacement(java.lang.String) java.util.regex.Matcher 'quoteReplacement' method])

==== Embedded pre-parsing rules ====

===== ''otherPreparsingRules'' definition =====

 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <PreparsingRules id="OTHER_PRE_RULES" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="preParsingRules.xsd">
 	<Version>1.1.1</Version>
 	<Author>Fabio Fiorellato</Author>
 	<Description>A few additional rules suggested by Fabio Fiorellato</Description>
 	<PreparsingRule id="1">
 		<Description>Removes juvenile / unidentified patterns</Description>
 		<Match>juv/unident$|juv$|[J|j]uvenile[s]?|(\s)juv(\s)|[U|u]nidentified [a-zA-Z]+|[U|u]nidentifiable|unident$|(\s)unident(\s)</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="2">
 		<Description>Removes SPP / CFF / AFF</Description>
 		<Match>(^|\s)[sS][pP][pP]?($|\s|\.)|(^|\s)[cC][fF][fF]?($|\s|\.)|(^|\s)[aA][fF][fF]?($|\s|\.)</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="3">
 		<Description>Removes dangling chars</Description>
 		<Match>(^|\s)[a-zA-Z]([^\p{L}]|$|\s)</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="4">
 		<Description>Removes possible acronyms</Description>
 		<Match>((^|\s)DWH|dwh|RW|rw($|\s|\.))|((\s)[A-Z]{2,3}($|\s|\.))</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="5">
 		<Description>Removes quotes</Description>
 		<Match>\"</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="6">
 		<Description>Removes misplaced commas</Description>
 		<Match>^\,|\,$</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="7">
 		<Description>Repairs missing closing bracket</Description>
 		<Match>(.*)\(([^\)]+)$</Match>
 		<Transform>$1($2)</Transform>
 	</PreparsingRule>
 </PreparsingRules>

===== ''bionymPreparsingRules'' definition =====

 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <PreparsingRules id="BIONYM_PRE_RULES" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="preParsingRules.xsd">
 	<Version>1.1.1</Version>
 	<Author>Edward Vanden Berghe</Author>
 	<Description>A few specific rules extracted from Edward's bionym.r</Description>
 	<PreparsingRule id="1">
 		<Description>Uncertain identification</Description>
 		<Match>[?]</Match>
 		<Transform></Transform>
 	</PreparsingRule>
 	<PreparsingRule id="2">
 		<Description>Drop subspecies indication</Description>
 		<Match> ssp.? </Match>
 		<Transform></Transform>
 	</PreparsingRule>
 	<PreparsingRule id="3">
 		<Description>Standardise variety indication</Description>
 		<Match> v(ar)?\\.? </Match>
 		<Transform> v. </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="4">
 		<Description>Standardise form indication</Description>
 		<Match> f(orm(a)?)?.? </Match>
 		<Transform> f. </Transform>
 	</PreparsingRule>
 </PreparsingRules>

===== ''commonPreparsingRules'' definition =====

 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <PreparsingRules id="COMMON_PRE_RULES" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="preParsingRules.xsd">
 	<Version>1.1.1</Version>
 	<Author>Edward Vanden Berghe</Author>
 	<Description>A few generic rules extracted from Edward's bionym.r</Description>
 	<PreparsingRule id="1">
 		<Description>Collapses multiple spaces</Description>
 		<Match>\s{2,}</Match>
 		<Transform> </Transform>
 	</PreparsingRule>
 	<PreparsingRule id="2">
 		<Description>Remove leading / trailing spaces</Description>
 		<Match>^\s|\s$</Match>
 		<Transform></Transform>
 	</PreparsingRule>
 </PreparsingRules>

=== Pre-parsing rules XSD ===

This is the XSD describing the structure of the pre-parsing ruleset xml: 

    <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
    <xs:schema version="1.0" xmlns:xs="http://www.w3.org/2001/XMLSchema">
        <xs:element name="PreparsingRules" type="preparsingRules"/>
 
        <xs:complexType name="preparsingRules">
            <xs:complexContent>
                <xs:extension base="Ruleset">
                    <xs:sequence>
                        <xs:element name="PreparsingRule" type="GeneralRule" maxOccurs="unbounded"/>
                    </xs:sequence>
                </xs:extension>
            </xs:complexContent>
        </xs:complexType>
 
        <xs:complexType name="Ruleset" abstract="true">
            <xs:sequence>
                <xs:element name="Version" type="xs:string"/>
                <xs:element name="Author" type="xs:string"/>
                <xs:element name="Description" type="xs:string"/>
            </xs:sequence>
            <xs:attribute name="id" type="xs:string" use="required"/>
        </xs:complexType>
 
        <xs:complexType name="GeneralRule">
            <xs:complexContent>
                <xs:extension base="Rule">
                    <xs:sequence/>
                </xs:extension>
            </xs:complexContent>
        </xs:complexType>
 
        <xs:complexType name="Rule">
            <xs:sequence>
                <xs:element name="Description" type="xs:string" minOccurs="0"/>
                <xs:element name="Match" type="xs:string"/>
                <xs:element name="Transform" type="xs:string"/>
            </xs:sequence>
            <xs:attribute name="id" type="xs:string" use="required"/>
        </xs:complexType>
    </xs:schema>

=== Post-parsing rules ===

Post-parsing rules will transform the parsed data (either the parsed scientific name or the parsed authority).

Conceptually they are identical to [[#Pre-parsing rules|pre-parsing rules]], with the exception that they're targeted to one specific section of the '''''parsed''''' data (either the scientific name or the author).

An example of (dummy) post-parsing rule is:

 <PostparsingRule id="foo">
        <Description>Dummy regexp</Description>
        <Match>[0-9]+</Match>
        <Transform> </Transform>
        <Target>parsedAuthority</Target>
 </Postparsing>

that will replace with blanks all digits in the input data 'parsed author' section.

==== Embedded post-parsing rulesets ====

===== ''bionymPostparsingRules'' definition =====

 <PostparsingRules id="BIONYM_POST_RULES" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="postParsingRules.xsd">
        <Version>1.1.1</Version>
        <Author>Edward Vanden Berghe</Author>
        <Description>A few rules extracted from Edward's bionym.r</Description>
        <PostparsingRule id="1">
                <Description>Remove temporary species indication</Description>
                <Match> sp[\\.]?( ?[1-9a-zA-Z])?$</Match>
                <Transform></Transform>
                <Target>parsedScientificName</Target>
        </PostparsingRule>
 </PostparsingRules>

=== Post-parsing rules XSD ===

This is the XSD describing the structure of the post-parsing ruleset xml:

    <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
    <xs:schema version="1.0" xmlns:xs="http://www.w3.org/2001/XMLSchema">
 
        <xs:element name="PostparsingRules" type="postparsingRules"/>
 
        <xs:complexType name="postparsingRules">
            <xs:complexContent>
                <xs:extension base="Ruleset">
                    <xs:sequence>
                        <xs:element name="PostparsingRule" type="TargetedRule" maxOccurs="unbounded"/>
                    </xs:sequence>
                </xs:extension>
            </xs:complexContent>
        </xs:complexType>
 
        <xs:complexType name="Ruleset" abstract="true">
            <xs:sequence>
                <xs:element name="Version" type="xs:string"/>
                <xs:element name="Author" type="xs:string"/>
                <xs:element name="Description" type="xs:string"/>
            </xs:sequence>
            <xs:attribute name="id" type="xs:string" use="required"/>
        </xs:complexType>
 
        <xs:complexType name="TargetedRule">
            <xs:complexContent>
                <xs:extension base="Rule">
                    <xs:sequence>
                        <xs:element name="Target" type="ruleTargets"/>
                    </xs:sequence>
                </xs:extension>
            </xs:complexContent>
        </xs:complexType>
 
        <xs:complexType name="Rule">
            <xs:sequence>
                <xs:element name="Description" type="xs:string" minOccurs="0"/>
                <xs:element name="Match" type="xs:string"/>
                <xs:element name="Transform" type="xs:string"/>
            </xs:sequence>
            <xs:attribute name="id" type="xs:string" use="required"/>
        </xs:complexType>
 
        <xs:simpleType name="ruleTargets">
            <xs:restriction base="xs:string">
                <xs:enumeration value="parsedScientificName"/>
                <xs:enumeration value="parsedAuthority"/>
            </xs:restriction>
        </xs:simpleType>
    </xs:schema>

== Download ==

You can download the [[ YASMEEN ]] input data parser through one of this URLs:

* [http://goo.gl/XwMnDB v1.1.1] (2.796KB)