Difference between revisions of "FishFinderTMPlugin"

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Species TM Plugin is a plugin of the [[Tree-Based_Access | Tree Based Access Facilities]] that defines and maintains tree views of biodiversity data sources exposed by the Species Manager services.  
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FishFinder TM Plugin (it was erroneously named FIGIS until gCube 2.17) is a plugin of the [[Tree-Based_Access | Tree Based Access Facilities]] that defines and maintains tree views of factsheets produced by the FIGIS group and exposed by the [http://figisapps.fao.org/vrmf/samples/species/FS/ FIGIS APIs].
Species TM Plugin provides an uniform model to access and storage data from SPD Service.
+
Each Taxon generated via SPD Service is trasformed in a edge-labelled tree by Species TM Plugin.
+
  
==Tree model==
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Each fact sheet retrieved by FIGIS APIs is transformed in an edge-labelled tree by FishFinder TM Plugin.
  
A tree generated by SpeciesTMPlugin has three subtrees:
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== Plugin parameters fields ==
 +
The Plugin requires two parameters:
 +
* '''''source name''''': a name of the source; it will be used as identifier for the collection, e.g. "c13e3995-c85f-4cac-a026-e9e1ab6906d5";
 +
* '''''description''''': information about the source.
  
* DwC: each data from SPD Service is mapped to Darwin Core concepts (a detailed description of the Darwin Core fields is listed [[Checklist_DwC | here]]):
+
== Tree model ==
** [http://rs.tdwg.org/dwc/terms/Taxon  Taxon]: [http://rs.tdwg.org/dwc/terms/scientificNameID scientificNameID] | [http://rs.tdwg.org/dwc/terms/acceptedNameUsageID acceptedNameUsageID] | [http://rs.tdwg.org/dwc/terms/parentNameUsageID parentNameUsageID] | [http://rs.tdwg.org/dwc/terms/scientificName scientificName] | [http://rs.tdwg.org/dwc/terms/nameAccordingTo nameAccordingTo] | [http://rs.tdwg.org/dwc/terms/kingdom kingdom] | [http://rs.tdwg.org/dwc/terms/phylum phylum] | [http://rs.tdwg.org/dwc/terms/class class] | [http://rs.tdwg.org/dwc/terms/order order] | [http://rs.tdwg.org/dwc/terms/family family] | [http://rs.tdwg.org/dwc/terms/genus genus] | [http://rs.tdwg.org/dwc/terms/subgenus subgenus] | [http://rs.tdwg.org/dwc/terms/specificEpithet specificEpithet] | [http://rs.tdwg.org/dwc/terms/infraspecificEpithet infraspecificEpithet] | [http://rs.tdwg.org/dwc/terms/taxonRank taxonRank] | [http://rs.tdwg.org/dwc/terms/verbatimTaxonRank verbatimTaxonRank] | [http://rs.tdwg.org/dwc/terms/scientificNameAuthorship scientificNameAuthorship] | [http://rs.tdwg.org/dwc/terms/taxonomicStatus taxonomicStatus] | [http://rs.tdwg.org/dwc/terms/taxonRemarks taxonRemarks] | [http://purl.org/dc/terms/modified modified] | [http://purl.org/dc/terms/rightsHolder rightsHolder]
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=== Conceptual Schema ===
** [http://rs.gbif.org/terms/1.0/VernacularName VernacularNames]: [http://rs.tdwg.org/dwc/terms/vernacularName vernacularName] | [http://purl.org/dc/terms/language language] | [http://rs.tdwg.org/dwc/terms/locality locality]
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A tree generated by FishFinderTMPlugin has a flat structure that reflects the CSV file structure:
* Properties: additional data elements from SPD Service are stored in this subtree.
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*'''''title''''': name of the fact sheet composed by the scientific name with authorship information, e.g. "Sarda chiliensis (Cuvier, 1831) - Fact sheet";
* Provenance: information about provenance (wasDerivedFrom, wasGeneratedBy).
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*'''''three_alpha_code''''': three letters to identify the fact sheet;
 +
*'''''name_en''''': the english common name of the species which the fact sheet refers to;
 +
*'''''name_fr''''': the french common name of the species which the fact sheet refers to;
 +
*'''''name_es''''': the spanish common name of the species which the fact sheet refers to;
 +
*'''''images''''': url to the species image;
 +
*'''''scientific_name''''': the scientific name of the species which the fact sheet refers to;
 +
*'''''family''''': the scientific name of the family in which the scientific name is classified;
 +
*'''''personal_author''''': the authorship information for the scientific_name;
 +
*'''''year''''': the four-digit year in which the scientific name was published;
 +
*'''''diagnostic_features''''': information about the species;
 +
*'''''area_text''''': a free text area;
 +
*'''''habitat_bio''''': information about the habitat;
 +
*'''''interest_fisheries''''': information about the fishery;
 +
*'''''local_names''''': a list of couples "common name, country"; the country is where such common name is used.
 +
*'''''factsheet_url''''': url of the fact sheet;
 +
*'''''factsheet_id''''': the identifier of the fact sheet.
  
=== Generic model ===
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=== XML Schema ===
  
 
<source lang="xml">
 
<source lang="xml">
  
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified" >
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<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
       <xs:element name="t:root" >
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       <xs:element name="t:root">
 
               <xs:complexType>
 
               <xs:complexType>
 
                     <xs:sequence>
 
                     <xs:sequence>
                             <xs:element name="alpha_cod" type="xs:string" />
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                             <xs:element name="title" type="xs:string"/>
                             <xs:element name="name_en" type="xs:string" />
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                            <xs:element name="three_alpha_code" type="xs:string"/>
                             <xs:element name="name_fr" type="xs:string" />
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                             <xs:element name="name_en" type="xs:string"/>
                             <xs:element name="name_es" type="xs:string" />
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                             <xs:element name="name_fr" type="xs:string"/>
                             <xs:element name="images" type="xs:string" />
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                             <xs:element name="name_es" type="xs:string"/>
                             <xs:element name="scientific_name" type="xs:string" />
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                             <xs:element name="images" type="xs:string"/>
                             <xs:element name="family" type="xs:string" />
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                             <xs:element name="scientific_name" type="xs:string"/>
                             <xs:element name="personal_author" type="xs:string" />
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                             <xs:element name="family" type="xs:string"/>
                             <xs:element name="year" type="xs:int" />
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                             <xs:element name="personal_author" type="xs:string"/>
                             <xs:element name="diagnostic_features" type="xs:string" />
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                             <xs:element name="year" type="xs:gYear"/>
                             <xs:element name="area_text" type="xs:string" />
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                             <xs:element name="diagnostic_features" type="xs:string"/>
                             <xs:element name="habitat_bio" type="xs:string" />
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                             <xs:element name="area_text" type="xs:string"/>
                             <xs:element name="interest_fisheries" type="xs:string" />
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                             <xs:element name="habitat_bio" type="xs:string"/>
                             <xs:element name="local_names" type="xs:string" />
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                             <xs:element name="interest_fisheries" type="xs:string"/>
                             <xs:element name="factsheet_url" type="xs:string" />
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                             <xs:element name="local_names" type="xs:string"/>
                             <xs:element name="factsheet_id" />
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                             <xs:element name="factsheet_url" type="xs:anyURI"/>
 +
                             <xs:element name="factsheet_id" type="xs:string"/>
 
                         </xs:sequence>
 
                         </xs:sequence>
                     <xs:attribute name="xmlns:t" type="xs:string" />
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                     <xs:attribute name="xmlns:t" type="xs:string"/>
                     <xs:attribute name="t:id" type="xs:string" />
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                     <xs:attribute name="t:id" type="xs:string"/>
 +
                    <xs:attribute name="t:source" type="xs:string"/>
 
                 </xs:complexType>
 
                 </xs:complexType>
 
           </xs:element>
 
           </xs:element>
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=== Example ===
 
=== Example ===
  
A tree generated by Figis TM Plugin looks like this:
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A tree generated by FishFinder TM Plugin looks like this:
  
 
<source lang="xml">
 
<source lang="xml">
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<?xml version="1.0" ?>
 
<?xml version="1.0" ?>
  
<t:root xmlns:t="http://gcube-system.org/namespaces/data/trees" t:id="BEP">
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<t:root xmlns:t="http://gcube-system.org/namespaces/data/trees" t:id="BEP" t:source="c13e3995-c85f-4cac-a026-e9e1ab6906d5">
  
<alpha_cod>BEP</alpha_cod>
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<title>Sarda chiliensis (Cuvier, 1831) - Fact sheet</title>
 +
<three_alpha_code>BEP</three_alpha_code>
 
<name_en>Eastern Pacific bonito</name_en>
 
<name_en>Eastern Pacific bonito</name_en>
 
<name_fr>Bonite du Pacifique oriental</name_fr>
 
<name_fr>Bonite du Pacifique oriental</name_fr>
 
<name_es>Bonito del Pacífico oriental</name_es>
 
<name_es>Bonito del Pacífico oriental</name_es>
<images>figis/species/images/Sarda/sco_sar_chi_web_3275_0.gif</images>
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<images>http://www.fao.org/figis/species/images/Sarda/sco_sar_chi_web_3275_0.gif</images>
 
<scientific_name>Sarda chiliensis</scientific_name>
 
<scientific_name>Sarda chiliensis</scientific_name>
 
<family>Scombridae</family>
 
<family>Scombridae</family>
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</source>
 
</source>
 
==Bind request==
 
 
An Activation Record allows the creation of collections. Using an Activation Record the user selects scientific names and data sources to create the collection.
 
 
A request has this form:
 
 
        '''List<ScientificName>''' as ScientificName in '''List<DataSource>''' return Taxon
 
 
If '''List<DataSource>''' is empty, Species TM Plugin will retrieve data from all Data Sources.
 
 
 
Examples:
 
 
        'Carcharodon carcharias' , 'Rosa' in '''ITIS, CatalogueOfLife''' return Taxon
 
 
        'Carcharodon carcharias' , 'Rosa' return Taxon
 
 
        'Carcharodon carcharias' return Taxon
 
  
 
==Maven coordinates==
 
==Maven coordinates==
  
The Maven coordinates of species-tree-plugin of its development versions are:  
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The Maven coordinates of fishfinder-tm-plugin of its development versions will be:  
  
 
<source lang="xml">
 
<source lang="xml">
  
 
<groupId>org.gcube.data.access</groupId>
 
<groupId>org.gcube.data.access</groupId>
<artifactId>species-tree-plugin</artifactId>
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<artifactId>fishfinder-tm-plugin</artifactId>
<version>1.1.0</version>
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<version>[1.2.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
  
 
</source>
 
</source>
  
The request classes are separated from the species-tree-plugin, in a component upon which plugin depends. This component is species-tree-requests.
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Until gCube 2.17 fishfinder-tm-plugin was called figis-tm-plugin and its coordinates were:
 
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The Maven coordinates of species-tree-requests of its development versions are:  
+
  
 
<source lang="xml">
 
<source lang="xml">
  
 
<groupId>org.gcube.data.access</groupId>
 
<groupId>org.gcube.data.access</groupId>
<artifactId>species-tree-requests</artifactId>
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<artifactId>figis-tm-plugin</artifactId>
<version>1.0.0-SNAPSHOT</version>
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<version>[1.0.0-SNAPSHOT,1.2.0-SNAPSHOT)</version>
  
 
</source>
 
</source>

Latest revision as of 15:21, 23 October 2013

FishFinder TM Plugin (it was erroneously named FIGIS until gCube 2.17) is a plugin of the Tree Based Access Facilities that defines and maintains tree views of factsheets produced by the FIGIS group and exposed by the FIGIS APIs.

Each fact sheet retrieved by FIGIS APIs is transformed in an edge-labelled tree by FishFinder TM Plugin.

Plugin parameters fields

The Plugin requires two parameters:

  • source name: a name of the source; it will be used as identifier for the collection, e.g. "c13e3995-c85f-4cac-a026-e9e1ab6906d5";
  • description: information about the source.

Tree model

Conceptual Schema

A tree generated by FishFinderTMPlugin has a flat structure that reflects the CSV file structure:

  • title: name of the fact sheet composed by the scientific name with authorship information, e.g. "Sarda chiliensis (Cuvier, 1831) - Fact sheet";
  • three_alpha_code: three letters to identify the fact sheet;
  • name_en: the english common name of the species which the fact sheet refers to;
  • name_fr: the french common name of the species which the fact sheet refers to;
  • name_es: the spanish common name of the species which the fact sheet refers to;
  • images: url to the species image;
  • scientific_name: the scientific name of the species which the fact sheet refers to;
  • family: the scientific name of the family in which the scientific name is classified;
  • personal_author: the authorship information for the scientific_name;
  • year: the four-digit year in which the scientific name was published;
  • diagnostic_features: information about the species;
  • area_text: a free text area;
  • habitat_bio: information about the habitat;
  • interest_fisheries: information about the fishery;
  • local_names: a list of couples "common name, country"; the country is where such common name is used.
  • factsheet_url: url of the fact sheet;
  • factsheet_id: the identifier of the fact sheet.

XML Schema

<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified">
       <xs:element name="t:root">
              <xs:complexType>
                     <xs:sequence>
                            <xs:element name="title" type="xs:string"/>
                            <xs:element name="three_alpha_code" type="xs:string"/>
                            <xs:element name="name_en" type="xs:string"/>
                            <xs:element name="name_fr" type="xs:string"/>
                            <xs:element name="name_es" type="xs:string"/>
                            <xs:element name="images" type="xs:string"/>
                            <xs:element name="scientific_name" type="xs:string"/>
                            <xs:element name="family" type="xs:string"/>
                            <xs:element name="personal_author" type="xs:string"/>
                            <xs:element name="year" type="xs:gYear"/>
                            <xs:element name="diagnostic_features" type="xs:string"/>
                            <xs:element name="area_text" type="xs:string"/>
                            <xs:element name="habitat_bio" type="xs:string"/>
                            <xs:element name="interest_fisheries" type="xs:string"/>
                            <xs:element name="local_names" type="xs:string"/>
                            <xs:element name="factsheet_url" type="xs:anyURI"/>
                            <xs:element name="factsheet_id" type="xs:string"/>
                        </xs:sequence>
                     <xs:attribute name="xmlns:t" type="xs:string"/>
                     <xs:attribute name="t:id" type="xs:string"/>
                     <xs:attribute name="t:source" type="xs:string"/>
                 </xs:complexType>
          </xs:element>
   </xs:schema>

Example

A tree generated by FishFinder TM Plugin looks like this:

<?xml version="1.0" ?>
 
<t:root xmlns:t="http://gcube-system.org/namespaces/data/trees"	t:id="BEP" t:source="c13e3995-c85f-4cac-a026-e9e1ab6906d5">
 
	<title>Sarda chiliensis (Cuvier, 1831) - Fact sheet</title>
	<three_alpha_code>BEP</three_alpha_code>
	<name_en>Eastern Pacific bonito</name_en>
	<name_fr>Bonite du Pacifique oriental</name_fr>
	<name_es>Bonito del Pacífico oriental</name_es>
	<images>http://www.fao.org/figis/species/images/Sarda/sco_sar_chi_web_3275_0.gif</images>
	<scientific_name>Sarda chiliensis</scientific_name>
	<family>Scombridae</family>
	<personal_author>(Cuvier, 1831)</personal_author>
	<year>1831</year>
	<diagnostic_features>Upper jaw teeth 18 to 30; lower jaw teeth 14 to
		25; vomerine teeth absent; supramaxilla wide (Collette &amp; Chao,
		1975:fig. 32d) 23 to 27 gillrakers on first arch. First dorsal fin
		with 17 to 19 spines, length of fin base 26.7 to 31.4% of fork length
		; dorsal finlets usually 8; 12 to 15 rays in anal fin; anal finlets
		usually 6 or 7; pectoral fin rays 22 to 26, usually 24 or 25.
		Vertebrae 22 to 24 precaudal plus 20 to 23 caudal, total 42 to 46,
		usually 44 or 45. Colour: dorsal stripes slightly oblique.
	</diagnostic_features>
	<area_text>Restricted to the eastern Pacific Ocean (Collette &amp;
		Chao, 1975:fig. 70). Its geographical range includes a northern and a
		southern subspecies separated by a tropical population of Sarda
		orientalis . The southern subspecies S. chiliensis chiliensis, occurs
		from Mancora, Peru, just south of the Gulf of Guayaquil southward to
		Talcahuano, Chile. The northern subspecies S. chiliensis lineolata
		(Girard) occurs from off the coast of Alaska (60° 16'N, 145° 32'W)
		southward to Cabo San Lucas at the tip of Baja California (22° 20'N,
		112° 27'W and in the Revillagigedo Islands).</area_text>
	<habitat_bio>An epipelagic, neritic species attaining sexual maturity
		at about 2 years of age.</habitat_bio>
	<interest_fisheries>In California, eastern Pacific bonito is taken
		commercially by purse seiners, but is more important to the
		recreational hooks and lines fishery operating from private and party
		boats, piers and jetties, and from the shore (Yoshida, 1980:42). In
		the mid-sixties, the Chilean bonito fishery between lquique and
		Antofagasta expanded from an almost entirely artisanal activity with
		floating gillnets and small purse seines to an industrial operation
		with specialized bonito/tuna vessels (Yoshida, 1980:42). The landings
		of the northern subspecies ( S. c. lineolata ) in California and
		Mexico have fluctuated greatly over the last 50 years from less than 1
		000 metric tons to nearly 14 000 t in the early seventies, ranking in
		13th place (4 003 t worth $1 222 000) in total California landings of
		1976. The Peruvian landings of the southern subspecies ( S. c.
		chiliensis ) increased from almost nil in 1940 to a peak of 110 000 t
		per year in the early sixties, thereafter gradually dropping off to 40
		000 t in the mid-seventies (Yoshida, 1980:44). The world catch for the
		species as a whole was down to between 10 219 t in 1976 and 15 936 t
		in 1981, reaching 21 308 t in 1977 (FAO, 1983). The total catch
		reported for this species to FAO for 1999 was 3 187 t. The countries
		with the largest catches were Mexico (1 775 t) and Peru (948 t).
	</interest_fisheries>
	<local_names>Bonito (Chile),Bonito (Colombia),Bonito (Mexico),Aguadito
		(Peru),Chilensk bonit (Sweden),Pacific bonito (USA),Chilijskaya
		pelamida (Former ussr)</local_names>
	<factsheet_url>http://www.fao.org/fishery/species/3275/en
	</factsheet_url>
	<factsheet_id></factsheet_id>
 
</t:root>

Maven coordinates

The Maven coordinates of fishfinder-tm-plugin of its development versions will be:

<groupId>org.gcube.data.access</groupId>
<artifactId>fishfinder-tm-plugin</artifactId>
<version>[1.2.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>

Until gCube 2.17 fishfinder-tm-plugin was called figis-tm-plugin and its coordinates were:

<groupId>org.gcube.data.access</groupId>
<artifactId>figis-tm-plugin</artifactId>
<version>[1.0.0-SNAPSHOT,1.2.0-SNAPSHOT)</version>