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update to be compatible with the latest worms version

This commit is contained in:
lucio 2020-03-10 13:13:31 +01:00
parent 5eed4dbfc1
commit ff1ea51e30
24 changed files with 1722 additions and 182 deletions
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40
.classpath
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@ -1,10 +1,38 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" output="target/classes" path="src/main/java"/>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
<classpathentry kind="src" output="target/classes" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>

9
.settings/org.eclipse.jdt.core.prefs
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@ -1,5 +1,8 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.source=1.7
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8

37
pom.xml
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@ -5,13 +5,13 @@
<parent>
<artifactId>maven-parent</artifactId>
<groupId>org.gcube.tools</groupId>
<version>1.0.0</version>
<version>1.1.0</version>
<relativePath />
</parent>
<groupId>org.gcube.data.spd</groupId>
<artifactId>worms-spd-plugin</artifactId>
<version>1.8.0-SNAPSHOT</version>
<version>1.8.1-SNAPSHOT</version>
<name>worms-plugin</name>
<description>worms plugin for species manager service</description>
@ -41,35 +41,20 @@
<groupId>org.gcube.resources.discovery</groupId>
<artifactId>ic-client</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.axis/axis -->
<dependency>
<groupId>org.apache.axis</groupId>
<artifactId>axis</artifactId>
<version>1.4</version>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/javax.xml/jaxrpc-api -->
<dependency>
<groupId>javax.xml</groupId>
<artifactId>jaxrpc-api</artifactId>
<version>1.1</version>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-discovery/commons-discovery -->
<dependency>
<groupId>commons-discovery</groupId>
<artifactId>commons-discovery</artifactId>
<version>0.5</version>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/wsdl4j/wsdl4j -->
<dependency>
<groupId>wsdl4j</groupId>
<artifactId>wsdl4j</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.gcube.data.spd</groupId>
<artifactId>spd-model</artifactId>
@ -121,7 +106,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2</version>
<configuration>
<descriptors>
<descriptor>${distroDirectory}/descriptor.xml</descriptor>

41
src/main/java/de/uni_jena/cs/fusion/client/worms/AphiaAttributeSets.java Normal file
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@ -0,0 +1,41 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Collection;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class AphiaAttributeSets {
/**
* Unique and persistent identifier within WoRMS. Primary key in the
* database.
*/
@JsonProperty("AphiaID")
public int aphiaId;
@JsonProperty("Attributes")
public Collection<Attribute> attributes;
}

188
src/main/java/de/uni_jena/cs/fusion/client/worms/AphiaRecord.java Normal file
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@ -0,0 +1,188 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class AphiaRecord {
/**
* Unique and persistent identifier within WoRMS. Primary key in the
* database.
*/
@JsonProperty("AphiaID")
public long aphiaId;
/**
* HTTP URL to the AphiaRecord
*/
public String url;
/**
* the full scientific name without authorship
*/
@JsonProperty("scientificname")
public String scientificName;
/**
* the authorship information for the scientific name formatted according to
* the conventions of the applicable nomenclaturalCode
*/
public String authority;
/**
* the taxonomic rank of the most specific name in the scientific name
*/
@JsonProperty("rank")
public String taxonomicRank;
/**
* the status of the use of the scientific name (usually a taxonomic
* opinion). Additional technical statuses are (1) quarantined: hidden from
* public interface after decision from an editor and (2) deleted: AphiaID
* should NOT be used anymore, please replace it by the valid_AphiaID
*/
public String status;
public String taxonRankID;
public String parentNameUsageID;
/**
* the reason why a scientific name is unaccepted
*/
@JsonProperty("unacceptreason")
public String unacceptReason;
/**
* the AphiaID (for the scientific name) of the currently accepted taxon.
* NULL if there is no currently accepted taxon.
*/
@JsonProperty("valid_AphiaID")
public long validAphiaId;
/**
* the scientific name of the currently accepted taxon
*/
@JsonProperty("valid_name")
public String validName;
/**
* the authorship information for the scientific name of the currently
* accepted taxon
*/
@JsonProperty("valid_authority")
public String validAuthority;
/**
* the full scientific name of the kingdom in which the taxon is classified
*/
@JsonProperty("kingdom")
public String taxonomicKingdom;
/**
* the full scientific name of the phylum or division in which the taxon is
* classified
*/
@JsonProperty("phylum")
public String taxonomicPhylum;
/**
* the full scientific name of the class in which the taxon is classified
*/
@JsonProperty("class")
public String taxonomicClass;
/**
* the full scientific name of the order in which the taxon is classified
*/
@JsonProperty("order")
public String taxonomicOrder;
/**
* the full scientific name of the family in which the taxon is classified
*/
@JsonProperty("family")
public String taxonomicFamily;
/**
* the full scientific name of the genus in which the taxon is classified
*/
@JsonProperty("genus")
public String taxonomicGenus;
/**
* a bibliographic reference for the resource as a statement indicating how
* this record should be cited (attributed) when used
*/
public String citation;
/**
* LifeScience Identifier. Persistent GUID for an AphiaID
*/
public String lsid;
/**
* a boolean flag indicating whether the taxon is a marine organism, i.e.
* can be found in/above sea water. Possible values: 0/1/NULL
*/
public Boolean isMarine;
/**
* a boolean flag indicating whether the taxon occurrs in brackish habitats.
* Possible values: 0/1/NULL
*/
public Boolean isBrackish;
/**
* a boolean flag indicating whether the taxon occurrs in freshwater
* habitats, i.e. can be found in/above rivers or lakes. Possible values:
* 0/1/NULL
*/
public Boolean isFreshwater;
/**
* a boolean flag indicating the taxon is a terrestial organism, i.e.
* occurrs on land as opposed to the sea. Possible values: 0/1/NULL
*/
public Boolean isTerrestrial;
/**
* a flag indicating an extinct organism. Possible values: 0/1/NULL
*/
public Boolean isExtinct;
/**
* Type of match.
*/
@JsonProperty("match_type")
public MatchType matchType;
/**
* The most recent date-time in GMT on which the resource was changed
*/
public String modified;
}

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src/main/java/de/uni_jena/cs/fusion/client/worms/Attribute.java Normal file
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@ -0,0 +1,90 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Collection;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class Attribute {
/**
* Unique and persistent identifier within WoRMS. Primary key in the
* database.
*/
@JsonProperty("AphiaID")
public int aphiaId;
/**
* The corresponding AttributeKey its measurementTypeID
*/
@JsonProperty("measurementTypeID")
public int measurementTypeId;
/**
* The corresponding AttributeKey its measurementType
*/
public String measurementType;
/**
* The value of the measurement, fact, characteristic, or assertion
*/
public String measurementValue;
/**
* The identifier for the AphiaSource for this attribute
*/
@JsonProperty("source_id")
public Integer sourceId;
/**
* The AphiaSource reference for this attribute
*/
public String reference;
/**
* Quality status of the record. Possible values: 'checked’, ‘trusted’ or
* 'unreviewed’. See http://www.marinespecies.org/aphia.php?p=manual#topic22
*/
@JsonProperty("qualitystatus")
public String qualityStatus;
/**
* The category identifier to list possible attribute values for this
* attribute definition
*/
@JsonProperty("CategoryID")
public Integer categoryID;
/**
* The AphiaID from where this attribute is inherited
*/
@JsonProperty("AphiaID_Inherited")
public Integer aphiaIdInherited;
/**
* The possible child attributes that help to describe to current attribute
*/
public Collection<Attribute> children;
}

59
src/main/java/de/uni_jena/cs/fusion/client/worms/AttributeKey.java Normal file
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@ -0,0 +1,59 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Collection;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class AttributeKey {
/**
* An internal identifier for the measurementType
*/
@JsonProperty("measurementTypeID")
public int measurementTypeId;
/**
* The nature of the measurement, fact, characteristic, or assertion http://www.marinespecies.org/traits/wiki
*/
public String measurementType;
/**
* The data type that is expected as value for this attribute definition
*/
@JsonProperty("input_id")
public int inputId;
/**
* The category identifier to list possible attribute values for this attribute definition
*/
@JsonProperty("CategoryID")
public int categoryId;
/**
* The possible child attribute keys that help to describe to current attribute
*/
public Collection<AttributeKey> children;
}

53
src/main/java/de/uni_jena/cs/fusion/client/worms/AttributeValue.java Normal file
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@ -0,0 +1,53 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Collection;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class AttributeValue {
/**
* An identifier for facts stored in the column measurementValue
*/
@JsonProperty("measurementValueID")
public int measurementValueId;
/**
* The value of the measurement, fact, characteristic, or assertion
*/
public String measurementValue;
/**
* Additional info/code that helps to the describe/define the
* measurementValue
*/
public String measurementValueCode;
/**
* Child measurementValues that are more specific
*/
public Collection<AttributeValue> children;
}

47
src/main/java/de/uni_jena/cs/fusion/client/worms/Classification.java Normal file
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@ -0,0 +1,47 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class Classification {
/**
* Unique and persistent identifier within WoRMS. Primary key in the
* database.
*/
@JsonProperty("AphiaID")
public int aphiaId;
/**
* the taxonomic rank of the most specific name in the scientific name
*/
@JsonProperty("rank")
public String taxonomicRank;
/**
* the full scientific name without authorship
*/
@JsonProperty("scientificname")
public String scientificName;
public Classification child;
}

88
src/main/java/de/uni_jena/cs/fusion/client/worms/Distribution.java Normal file
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@ -0,0 +1,88 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class Distribution {
/**
* The specific description of the place
*/
public String locality;
/**
* An identifier for the locality. Using the Marine Regions Geographic
* IDentifier (MRGID), see http://www.marineregions.org/mrgid.php
*/
public String locationID;
/**
* A geographic name less specific than the information captured in the
* locality term. Possible values: an IHO Sea Area or Nation, derived from
* the MarineRegions gazetteer
*/
public String higherGeography;
/**
* An identifier for the geographic region within which the locality
* occurred, using MRGID
*/
public String higherGeographyID;
/**
* The status of the distribution record. Possible values are ‘valid’
* ,’doubtful’ or 'inaccurate’. See here for explanation of the statuses
*/
public String recordStatus;
/**
* The type status of the distribution. Possible values: ‘holotype’ or
* empty.
*/
public String typeStatus;
/**
* The process by which the biological individual(s) represented in the
* Occurrence became established at the location. Possible values: values
* listed as Origin in WRIMS
*/
public String establishmentMeans;
/**
* The geographic latitude (in decimal degrees, WGS84)
*/
public double decimalLatitude;
/**
* The geographic longitude (in decimal degrees, WGS84)
*/
public double decimalLongitude;
/**
* Quality status of the record. Possible values: 'checked’, ‘trusted’ or
* 'unreviewed’. See http://www.marinespecies.org/aphia.php?p=manual#topic22
*/
public String qualityStatus;
}

64
src/main/java/de/uni_jena/cs/fusion/client/worms/ExternalIdentifierSource.java Normal file
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@ -0,0 +1,64 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public enum ExternalIdentifierSource {
/**
* Barcode of Life Database (BOLD) TaxID
*/
bold,
/**
* Dyntaxa ID
*/
dyntaxa,
/**
* Encyclopedia of Life page identifier
*/
eol,
/**
* FishBase species ID
*/
fishbase,
/**
* IUCN Red List Identifier
*/
iucn,
/**
* Life Science Identifier
*/
lsid,
/**
* NCBI Taxonomy ID (Genbank)
*/
ncbi,
/**
* ITIS Taxonomic Serial Number
*/
tsn,
/**
* Global Invasive Species Database
*/
gisd
}

29
src/main/java/de/uni_jena/cs/fusion/client/worms/MatchType.java Normal file
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@ -0,0 +1,29 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public enum MatchType {
exact, like, phonetic, near_1, near_2
}

64
src/main/java/de/uni_jena/cs/fusion/client/worms/Source.java Normal file
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@ -0,0 +1,64 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class Source {
/**
* Unique identifier for the source within WoRMS.
*/
@JsonProperty("source_id")
public int sourceId;
/**
* Usage of the source for this taxon. See
* http://www.marinespecies.org/aphia.php?p=manual#topic6 for all values
*/
public String use;
/**
* Full citation string
*/
public String reference;
/**
* Page(s) where the taxon is mentioned
*/
public String page;
/**
* Direct link to the source record
*/
public String url;
/**
* External link (i.e. journal, data system, etc…)
*/
public String link;
/**
* Full text link (PDF)
*/
public String fulltext;
/**
* Digital Object Identifier
*/
public String doi;
}

34
src/main/java/de/uni_jena/cs/fusion/client/worms/Vernacular.java Normal file
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package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class Vernacular {
public String vernacular;
@JsonProperty("language_code")
public String languageCode;
public String language;
}

726
src/main/java/de/uni_jena/cs/fusion/client/worms/WormsClient.java Normal file
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@ -0,0 +1,726 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.IOException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLEncoder;
import java.time.DateTimeException;
import java.time.format.DateTimeFormatter;
import java.time.temporal.TemporalAccessor;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
/**
* <p>
* A client for the <a href="http://www.marinespecies.org/rest/">World Register
* of Marine Species REST API</a>. Please refer to the <a
* href=""http://www.marinespecies.org/about.php#terms>terms of use</a>.
* </p>
* <p>
* <b>Acknowledgments:</b> The development of the WoRMS Client was funded by DFG
* in the scope of the LakeBase project within the Scientific Library Services
* and Information Systems (LIS) program.
* </p>
*
* @author Jan Martin Keil
* @since 1.0.0
*/
public class WormsClient {
private final static int HTTP_MAX_URL_BYTES = 7806;
private final static String SERVICE_URL = "http://www.marinespecies.org/rest/";
private final static ObjectMapper JSON = new ObjectMapper();
/**
* Constructs a {@link WormsClient} with a default {@link CloseableHttpClient}
* configured to a maximum number of 10 connections.
*
* @since 1.0.0
*/
public WormsClient() {}
/**
* Get attribute definitions. To refer to root items specify ID = ‘0’.
*
* @param id
* The attribute definition id to search for
* @param includeChildren
* Include the tree of children.
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AttributeKey> aphiaAttributeKeysById(long id, boolean includeChildren)
throws WormsClientException {
return this.request(
SERVICE_URL + "AphiaAttributeKeysByID/" + id + ((includeChildren) ? "?include_inherited=true" : ""),
new TypeReference<ArrayList<AttributeKey>>() {
});
}
/**
* Get a list of attributes for a given AphiaID
*
* @param aphiaId
* The AphiaID to search for
* @param includeChildren
* Include attributes inherited from the taxon its parent(s).
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<Attribute> aphiaAttributesByAphiaId(long aphiaId, boolean includeChildren)
throws WormsClientException {
return this.request(
SERVICE_URL + "AphiaAttributesByAphiaID/" + aphiaId
+ ((includeChildren) ? "?include_inherited=true" : ""),
new TypeReference<ArrayList<Attribute>>() {
});
}
/**
* Get list values that are grouped by an CateogryID
*
* @param id
* The CateogryID to search for
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AttributeValue> aphiaAttributeValuesByCategoryId(long id) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaAttributeValuesByCategoryID/" + id,
new TypeReference<ArrayList<AttributeValue>>() {
});
}
/**
* <p>
* Get the direct children for a given AphiaID.
* </p>
*
* <p>
* <b>Note:</b> This methods might cause multiple calls of
* {@link #aphiaChildrenByAphiaId(long, boolean, long)} to receive all records
* in chunks of 50 records.
* </p>
*
* @param aphiaId
* The AphiaID to search for
* @param marineOnly
* Limit to marine taxa.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaChildrenByAphiaId(long aphiaId, boolean marineOnly)
throws WormsClientException {
Collection<AphiaRecord> totalResult = new ArrayList<AphiaRecord>();
Collection<AphiaRecord> singleResult;
long offset = 1;
do {
singleResult = aphiaChildrenByAphiaId(aphiaId, marineOnly, offset);
totalResult.addAll(singleResult);
offset += 50;
} while (singleResult.size() == 50);
return totalResult;
}
/**
* Get the direct children (max. 50) for a given AphiaID.
*
* @param aphiaId
* The AphiaID to search for
* @param marineOnly
* Limit to marine taxa.
* @param offset
* Starting recordnumber, when retrieving next chunk of 50 records.
* First record has number {@code 1}.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaChildrenByAphiaId(long aphiaId, boolean marineOnly, long offset)
throws WormsClientException {
return this.request(
SERVICE_URL + "AphiaChildrenByAphiaID/" + aphiaId + "?marine_only=" + marineOnly + "&offset=" + offset,
new TypeReference<ArrayList<AphiaRecord>>() {
});
}
/**
* Get the complete classification for one taxon. This also includes any sub or
* super ranks.
*
* @param aphiaId
* The AphiaID to search for
* @return classification of the taxon
* @throws WormsClientException
*
* @since 1.0.0
*/
public Classification aphiaClassificationByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaClassificationByAphiaID/" + aphiaId,
new TypeReference<Classification>() {
});
}
/**
* Get all distributions for a given AphiaID External Identifiers
*
* @param aphiaId
* The AphiaID to search for
* @return all distributions
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<Distribution> aphiaDistributionsByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaDistributionsByAphiaID/" + aphiaId,
new TypeReference<ArrayList<Distribution>>() {
});
}
/**
* Get any external identifier(s) for a given AphiaID
*
* @param aphiaId
* The AphiaID to search for
* @param type
* Type of external identifier to return.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<String> aphiaExternalIdByAphiaId(long aphiaId, ExternalIdentifierSource type)
throws WormsClientException {
return this.request(SERVICE_URL + "AphiaExternalIDByAphiaID/" + aphiaId + "?type=" + type.name(),
new TypeReference<ArrayList<String>>() {
});
}
/**
* Get the AphiaID for a given name
*
* @param scientificName
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Long aphiaIdByName(String scientificName) throws WormsClientException {
try {
return this.request(
SERVICE_URL + "AphiaIDByName/" + URLEncoder.encode(scientificName, "UTF-8").replace("+", "%20"),
new TypeReference<Long>() {
});
} catch (UnsupportedEncodingException e) {
throw new WormsClientException(e);
}
}
/**
* <p>
* Get a list of AphiaIDs with attribute tree for a given attribute definition
* ID Distributions.
* </p>
*
* <p>
* <b>Note:</b> This methods might cause multiple calls of
* {@link #aphiaIdsByAttributeKeyId(long, long)} to receive all records in
* chunks of 50 records.
* </p>
*
* @param id
* The attribute definition id to search for
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaAttributeSets> aphiaIdsByAttributeKeyId(long id) throws WormsClientException {
Collection<AphiaAttributeSets> totalResult = new ArrayList<AphiaAttributeSets>();
Collection<AphiaAttributeSets> singleResult;
long offset = 1;
do {
singleResult = aphiaIdsByAttributeKeyId(id, offset);
totalResult.addAll(singleResult);
offset += 50;
} while (singleResult.size() == 50);
return totalResult;
}
/**
* Get a list of AphiaIDs (max 50) with attribute tree for a given attribute
* definition ID Distributions.
*
* @param id
* The attribute definition id to search for
* @param offset
* Starting record number, when retrieving next chunk of (50)
* records. First record has number {@code 1}.
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaAttributeSets> aphiaIdsByAttributeKeyId(long id, long offset) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaIDsByAttributeKeyID/" + id,
new TypeReference<ArrayList<AphiaAttributeSets>>() {
});
}
/**
* Get the name for a given AphiaID
*
* @param aphiaId
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public String aphiaNameByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaNameByAphiaID/" + aphiaId, new TypeReference<String>() {
});
}
/**
* Get the complete AphiaRecord for a given AphiaID
*
* @param aphiaId
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public AphiaRecord aphiaRecordByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaRecordByAphiaID/" + aphiaId, new TypeReference<AphiaRecord>() {
});
}
/**
* Get the Aphia Record for a given external identifier Sources
*
* @param id
* @param type
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public AphiaRecord aphiaRecordByExternalId(String id, ExternalIdentifierSource type) throws WormsClientException {
try {
return this
.request(
SERVICE_URL + "AphiaRecordByExternalID/"
+ URLEncoder.encode(id, "UTF-8").replace("+", "%20") + "?type=" + type.name(),
new TypeReference<AphiaRecord>() {
});
} catch (UnsupportedEncodingException e) {
throw new WormsClientException(e);
}
}
/**
* <p>
* Lists all AphiaRecords (max. 50) modified or added between a specific time
* interval
* </p>
*
* <p>
* <b>Note:</b> This methods might cause multiple request to receive all records
* in chunks of 50 records.
* </p>
*
* @param statdate
* @param enddate
* @param marineOnly
* Limit to marine taxa.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaRecordsByDate(TemporalAccessor statdate, TemporalAccessor enddate,
boolean marineOnly) throws WormsClientException {
Collection<AphiaRecord> totalResult = new ArrayList<AphiaRecord>();
Collection<AphiaRecord> singleResult;
long offset = 1;
do {
singleResult = aphiaRecordsByDate(statdate, enddate, marineOnly, offset);
totalResult.addAll(singleResult);
offset += 50;
} while (singleResult.size() == 50);
return totalResult;
}
/**
* Lists all AphiaRecords (max. 50) modified or added between a specific time
* interval
*
* @param statdate
* @param enddate
* @param marineOnly
* Limit to marine taxa.
* @param offset
* Starting record number, when retrieving next chunk of (50)
* records. First record has number {@code 1}.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaRecordsByDate(TemporalAccessor statdate, TemporalAccessor enddate,
boolean marineOnly, long offset) throws WormsClientException {
try {
return this.request(SERVICE_URL + "AphiaRecordsByDate?startdate="
+ DateTimeFormatter.ISO_OFFSET_DATE_TIME.format(statdate) + "&enddate="
+ DateTimeFormatter.ISO_OFFSET_DATE_TIME.format(enddate) + "&marine_only=" + marineOnly + "&offset="
+ offset, new TypeReference<ArrayList<AphiaRecord>>() {
});
} catch (DateTimeException e) {
throw new WormsClientException(e);
}
}
/**
* <p>
* For each given scientific name (may include authority), try to find one or
* more AphiaRecords, using the TAXAMATCH fuzzy matching algorithm by Tony Rees.
* This allows you to (fuzzy) match multiple names in one call.
* </p>
*
* <p>
* <b>Note:</b> This methods might cause multiple service request.
* </p>
*
* @param scientificNames
* Names to search for
* @param marineOnly
* Limit to marine taxa.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public List<Collection<AphiaRecord>> aphiaRecordsByMatchNames(List<String> scientificNames, boolean marineOnly)
throws WormsClientException {
return requestPartitioned(SERVICE_URL + "AphiaRecordsByMatchNames?scientificnames[]=", scientificNames,
"&scientificnames[]=", 50, "&marine_only=" + marineOnly);
}
/**
* <p>
* Get one or more matching AphiaRecords for a given name.
* </p>
*
* <p>
* <b>Note:</b> This methods might cause multiple calls of
* {@link #aphiaRecordsByName(String, boolean, boolean, long)} to receive all
* records in chunks of 50 records.
* </p>
*
* @param scientificName
* Name to search for
* @param like
* Add a "%"-sign added after the ScientificName (SQL LIKE function).
* @param marineOnly
* Limit to marine taxa.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaRecordsByName(String scientificName, boolean like, boolean marineOnly)
throws WormsClientException {
Collection<AphiaRecord> totalResult = new ArrayList<AphiaRecord>();
Collection<AphiaRecord> singleResult;
long offset = 1;
do {
singleResult = aphiaRecordsByName(scientificName, like, marineOnly, offset);
totalResult.addAll(singleResult);
offset += 50;
} while (singleResult.size() == 50);
return totalResult;
}
/**
* Get one or more matching AphiaRecords (max. 50) for a given name.
*
* @param scientificName
* Name to search for
* @param like
* Add a "%"-sign added after the ScientificName (SQL LIKE function).
* @param marineOnly
* Limit to marine taxa.
* @param offset
* Starting record number, when retrieving next chunk of (50)
* records. First record has number {@code 1}.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaRecordsByName(String scientificName, boolean like, boolean marineOnly,
long offset) throws WormsClientException {
try {
return this.request(
SERVICE_URL + "AphiaRecordsByName/"
+ URLEncoder.encode(Objects.requireNonNull(scientificName), "UTF-8").replace("+", "%20")
+ "?like=" + like + "&marine_only=" + marineOnly + "&offset=" + offset,
new TypeReference<ArrayList<AphiaRecord>>() {
});
} catch (UnsupportedEncodingException e) {
throw new WormsClientException(e);
}
}
/**
* For each given scientific name, try to find one or more AphiaRecords (max.
* 50). This allows you to match multiple names in one call. Limited to 500
* names at once for performance reasons.
*
* @param scientificNames
* Collection of names to search for
* @param like
* Add a "%"-sign added after the ScientificName (SQL LIKE function).
* @param marineOnly
* Limit to marine taxa.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public List<Collection<AphiaRecord>> aphiaRecordsByNames(List<String> scientificNames, boolean like,
boolean marineOnly) throws WormsClientException {
return requestPartitioned(SERVICE_URL + "AphiaRecordsByNames?scientificnames[]=", scientificNames,
"&scientificnames[]=", 500, "&like=" + like + "&marine_only=" + marineOnly);
}
/**
* <p>
* Get one or more Aphia Records for a given vernacular.
* </p>
*
* <p>
* <b>Note:</b> This methods might cause multiple request to receive all records
* in chunks of 50 records.
* </p>
*
* @param vernacular
* The vernacular to find records for
* @param like
* Add a "%"-sign before and after the input (SQL LIKE ‘%vernacular%’
* function).
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaRecordsByVernacular(String vernacular, boolean like)
throws WormsClientException {
Collection<AphiaRecord> totalResult = new ArrayList<AphiaRecord>();
Collection<AphiaRecord> singleResult;
long offset = 1;
do {
singleResult = aphiaRecordsByVernacular(vernacular, like, offset);
totalResult.addAll(singleResult);
offset += 50;
} while (singleResult.size() == 50);
return totalResult;
}
/**
*
* Get one or more Aphia Records (max. 50) for a given vernacular.
*
* @param vernacular
* The vernacular to find records for
* @param like
* Add a "%"-sign before and after the input (SQL LIKE ‘%vernacular%’
* function).
* @param offset
* Starting record number, when retrieving next chunk of (50)
* records. First record has number {@code 1}.
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaRecordsByVernacular(String vernacular, boolean like, long offset)
throws WormsClientException {
try {
return this.request(SERVICE_URL + "AphiaRecordsByVernacular/"
+ URLEncoder.encode(Objects.requireNonNull(vernacular), "UTF-8").replace("+", "%20") + "?like="
+ like + "&offset=" + offset, new TypeReference<ArrayList<AphiaRecord>>() {
});
} catch (UnsupportedEncodingException e) {
throw new WormsClientException(e);
}
}
/**
* Get one or more sources/references including links, for one AphiaID
*
* @param aphiaId
* The AphiaID to search for
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<Source> aphiaSourcesByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaSourcesByAphiaID/" + aphiaId, new TypeReference<ArrayList<Source>>() {
});
}
/**
* Get all synonyms for a given AphiaID.
*
* @param aphiaId
* The AphiaID to search for
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<AphiaRecord> aphiaSynonymsByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaSynonymsByAphiaID/" + aphiaId,
new TypeReference<ArrayList<AphiaRecord>>() {
});
}
/**
* Get all vernaculars for a given AphiaID
*
* @param aphiaId
* The AphiaID to search for
* @return
* @throws WormsClientException
*
* @since 1.0.0
*/
public Collection<Vernacular> aphiaVernacularsByAphiaId(long aphiaId) throws WormsClientException {
return this.request(SERVICE_URL + "AphiaVernacularsByAphiaID/" + aphiaId,
new TypeReference<ArrayList<Vernacular>>() {
});
}
@SuppressWarnings("unchecked")
private <T> List<Collection<T>> ensureEmptyCollections(List<Collection<T>> list, long count) {
if (list.isEmpty()) {
// add omitted empty collections
return Stream.generate(() -> {
return (Collection<T>) Collections.emptyList();
}).limit(count).collect(Collectors.toList());
} else {
return list;
}
}
@SuppressWarnings("unchecked")
private <T> T request(String url, TypeReference<T> t) throws WormsClientException {
try {
URL urlConn = new URL(url);
HttpURLConnection connection = (HttpURLConnection)urlConn.openConnection();
connection.setRequestMethod("GET");
connection.setDoOutput(true);
connection.setDoInput(true);
connection.setRequestProperty("Content-type", "application/json");
if (connection.getResponseCode() == 200) {
try (InputStream content = (InputStream)connection.getContent()) {
return JSON.readValue(content, t);
} catch (JsonParseException | JsonMappingException e) {
throw new WormsClientException("\"" + url + "\" returned invalid response.", e);
}
} else if (connection.getResponseCode() == 204) {
if (JSON.getTypeFactory().constructType(t).isContainerType()) {
try {
return (T) JSON.getTypeFactory().constructType(t).getRawClass().newInstance();
} catch (InstantiationException | IllegalAccessException | IllegalArgumentException
| SecurityException e) {
throw new WormsClientException("Failed to instantiate empty result for \"" + url + "\".", e);
}
} else {
return null;
}
} else {
throw new WormsClientException(
"\"" + url + "\" returned " + connection.getResponseCode() + ".");
}
} catch (IOException e) {
throw new WormsClientException("Request failed on \"" + url + "\".", e);
}
}
private List<Collection<AphiaRecord>> requestPartitioned(String requestPrefix, List<String> names,
String requestNameDelimiter, int maxNamesPerRequest, String requestPostfix) throws WormsClientException {
List<Collection<AphiaRecord>> totalResult = new ArrayList<Collection<AphiaRecord>>();
StringBuilder requestUrl = new StringBuilder(requestPrefix);
long requestNames = 0;
for (String scientificName : names) {
try {
String scientificNameEncoded = URLEncoder.encode(scientificName, "UTF-8").replace("+", "%20");
if (requestNames == maxNamesPerRequest || requestUrl.length() + requestNameDelimiter.length()
+ scientificNameEncoded.length() + requestPostfix.length() > HTTP_MAX_URL_BYTES) {
// reached max number of names per request or max length of URL
// request partial result and add to total results
totalResult.addAll(ensureEmptyCollections(this.request(requestUrl.append(requestPostfix).toString(),
new TypeReference<ArrayList<Collection<AphiaRecord>>>() {
}), requestNames));
// reset request
requestUrl = new StringBuilder(requestPrefix);
requestNames = 0;
}
if (requestNames != 0) {
requestUrl.append(requestNameDelimiter);
}
requestUrl.append(scientificNameEncoded);
requestNames++;
} catch (UnsupportedEncodingException e) {
throw new WormsClientException(e);
}
}
// request last partial result and add to total results
totalResult.addAll(ensureEmptyCollections(this.request(requestUrl.append(requestPostfix).toString(),
new TypeReference<ArrayList<Collection<AphiaRecord>>>() {
}), requestNames));
return totalResult;
}
}

45
src/main/java/de/uni_jena/cs/fusion/client/worms/WormsClientException.java Normal file
View File

@ -0,0 +1,45 @@
package de.uni_jena.cs.fusion.client.worms;
/*-
* #%L
* LakeBase Semantic Service
* %%
* Copyright (C) 2018 Heinz Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
/**
* @author Jan Martin Keil
* @since 1.0.0
*/
public class WormsClientException extends Exception {
private static final long serialVersionUID = -7269153574516662753L;
public WormsClientException() {
}
public WormsClientException(String message) {
super(message);
}
public WormsClientException(Throwable cause) {
super(cause);
}
public WormsClientException(String message, Throwable cause) {
super(message, cause);
}
}

52
src/main/java/org/gcube/data/spd/wormsplugin/Utils.java
View File

@ -1,9 +1,9 @@
package org.gcube.data.spd.wormsplugin;
import java.rmi.RemoteException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.List;
import org.gcube.data.spd.model.CommonName;
@ -14,25 +14,27 @@ import org.gcube.data.spd.model.products.TaxonomyStatus.Status;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import aphia.v1_0.worms.AphiaRecord;
import aphia.v1_0.worms.Classification;
import aphia.v1_0.worms.Vernacular;
import de.uni_jena.cs.fusion.client.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.Classification;
import de.uni_jena.cs.fusion.client.worms.Vernacular;
import de.uni_jena.cs.fusion.client.worms.WormsClientException;
public class Utils {
static Logger logger = LoggerFactory.getLogger(Utils.class);
public static Taxon retrieveTaxon(Classification classification, int aphiaID){
public static Taxon retrieveTaxon(Classification classification, long aphiaID){
Taxon taxon = null;
while (classification.getAphiaID()!=aphiaID){
Taxon newTaxon = new Taxon(classification.getAphiaID()+"");
while (classification.aphiaId!=aphiaID){
Taxon newTaxon = new Taxon(classification.aphiaId+"");
if (taxon!=null)
newTaxon.setParent(taxon);
newTaxon.setRank(classification.getRank());
newTaxon.setRank(classification.taxonomicRank);
// logger.trace(classification.getRank());
// logger.trace(classification.getScientificname());
newTaxon.setScientificName(classification.getScientificname());
classification = classification.getChild();
newTaxon.setScientificName(classification.scientificName);
classification = classification.child;
taxon = newTaxon;
}
// logger.trace(taxon);
@ -40,52 +42,52 @@ public class Utils {
}
public static TaxonomyItem retrieveTaxonomy(Classification classification, int aphiaID){
public static TaxonomyItem retrieveTaxonomy(Classification classification, long aphiaID){
List<CommonName> listCommNames = new ArrayList<CommonName> ();
TaxonomyItem taxon = null;
while (classification.getAphiaID()!=aphiaID){
while (classification.aphiaId!=aphiaID){
int id = classification.getAphiaID();
int id = classification.aphiaId;
TaxonomyItem newTaxon = new TaxonomyItem(id+"");
if (taxon!=null)
newTaxon.setParent(taxon);
newTaxon.setRank(classification.getRank());
newTaxon.setScientificName(classification.getScientificname());
newTaxon.setRank(classification.taxonomicRank);
newTaxon.setScientificName(classification.scientificName);
newTaxon.setCredits(Utils.createCredits());
AphiaRecord record = null;
try {
record = WormsPlugin.binding.getAphiaRecordByID(id);
record = WormsPlugin.wormsClient.aphiaRecordByAphiaId(id);
}catch (Exception e) {
logger.error("Error getAphiaRecordByID ", e);
}
if (record != null){
newTaxon.setCitation(record.getCitation());
newTaxon.setLsid(record.getLsid());
newTaxon.setScientificNameAuthorship(record.getAuthority());
newTaxon.setCitation(record.citation);
newTaxon.setLsid(record.lsid);
newTaxon.setScientificNameAuthorship(record.authority);
}
Vernacular[] vernaculars;
Collection<Vernacular> vernaculars;
try {
vernaculars = WormsPlugin.binding.getAphiaVernacularsByID(classification.getAphiaID());
vernaculars = WormsPlugin.wormsClient.aphiaVernacularsByAphiaId(classification.aphiaId);
if (vernaculars!=null){
// logger.debug("found vernacular name");
for (Vernacular vernacular : vernaculars) {
if (vernacular.getLanguage_code()!=null){
CommonName a = new CommonName(vernacular.getLanguage(),vernacular.getVernacular());
if (vernacular.languageCode!=null){
CommonName a = new CommonName(vernacular.language,vernacular.vernacular);
listCommNames.add(a);
}
}
}
} catch (RemoteException e) {
} catch (WormsClientException e) {
logger.error("RemoteException", e);
}
newTaxon.setCommonNames(listCommNames);
newTaxon.setStatus(new TaxonomyStatus("accepted", Status.ACCEPTED));
classification = classification.getChild();
classification = classification.child;
taxon = newTaxon;
}
return taxon;

86
src/main/java/org/gcube/data/spd/wormsplugin/WormsPlugin.java
View File

@ -3,6 +3,7 @@ package org.gcube.data.spd.wormsplugin;
import java.net.URL;
import java.rmi.RemoteException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
@ -31,36 +32,24 @@ import org.gcube.data.spd.wormsplugin.capabilities.NamesMappingImpl;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import aphia.v1_0.worms.AphiaRecord;
import aphia.v1_0.worms.Source;
import aphia.v1_0.worms.Vernacular;
import de.uni_jena.cs.fusion.client.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.Source;
import de.uni_jena.cs.fusion.client.worms.Vernacular;
import de.uni_jena.cs.fusion.client.worms.WormsClient;
import de.uni_jena.cs.fusion.client.worms.WormsClientException;
public class WormsPlugin extends AbstractPlugin {
private Logger logger = LoggerFactory.getLogger(WormsPlugin.class);
public static String credits = "This information object has been generated via the Species Product Discovery service on XDATEX by interfacing with World Register of Marine Species (http://www.marinespecies.org/)";
public static aphia.v1_0.worms.AphiaNameServiceBindingStub binding;
public static String baseurl;
public static WormsClient wormsClient;
@Override
public void initialize(ServiceEndpoint res) throws Exception {
setUseCache(true);
try {
for (AccessPoint ap:res.profile().accessPoints()) {
if (ap.name().equals("portType")){
baseurl = ap.address();
}
}
binding = (aphia.v1_0.worms.AphiaNameServiceBindingStub)
new aphia.v1_0.worms.AphiaNameServiceLocator().getAphiaNameServicePort(new URL(baseurl));
}
catch (javax.xml.rpc.ServiceException jre) {
logger.error("error contacting worms service", jre);
throw jre;
}
super.initialize(res);
wormsClient = new WormsClient();
}
@ -103,73 +92,74 @@ public class WormsPlugin extends AbstractPlugin {
DataProvider dp = new DataProvider("worms");
dp.setName("Worms");
AphiaRecord[] records = null;
Collection<AphiaRecord> records = null;
List<CommonName> listCommNames = new ArrayList<CommonName> ();
final int offsetlimit=50;
int offset =1;
do{
if (type.equals("vernacular"))
records = binding.getAphiaRecordsByVernacular(word, true, offset);
records = wormsClient.aphiaRecordsByVernacular(word, true, offset);
else if (type.equals("scientific"))
records = binding.getAphiaRecords(word, true, false, false, offset);
records = wormsClient.aphiaRecordsByName(word, true, false, offset);
if (records!=null){
for (AphiaRecord record : records){
//logger.debug("found record in worms");
Source[] sources = null;
Collection<Source> sources = null;
if (record==null || (sources= binding.getSourcesByAphiaID(record.getAphiaID()))==null || record.getScientificname()==null)
if (record==null || (sources= wormsClient.aphiaSourcesByAphiaId(record.aphiaId))==null || record.scientificName==null)
continue;
for (Source source : sources){
//logger.debug("found source in worms");
if (source==null)
continue;
if (source.getReference()!=null){
if (source.reference!=null){
// logger.debug("source has fulltext not null");
DataSet ds = new DataSet(record.getAphiaID()+"||"+source.getReference().hashCode());
ds.setName(source.getReference());
if (source.getUrl()!=null) ds.setCitation(source.getUrl());
DataSet ds = new DataSet(record.aphiaId+"||"+source.reference.hashCode());
ds.setName(source.reference);
if (source.url!=null) ds.setCitation(source.url);
ds.setDataProvider(dp);
ResultItem item = new ResultItem(record.getAphiaID()+"", record.getScientificname());
ResultItem item = new ResultItem(record.aphiaId+"", record.scientificName);
// Calendar now = Calendar.getInstance();
// SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
// String credits ="Biodiversity data published by: "+ds.getName()+" (Accessed through WoRMS web service, "+format.format(now.getTime())+")";
AphiaRecord[] synonyms = binding.getAphiaSynonymsByID(record.getAphiaID());
if (synonyms!=null && synonyms.length>0){
Collection<AphiaRecord> synonyms = wormsClient.aphiaSynonymsByAphiaId(record.aphiaId);
if (synonyms!=null && synonyms.size()>0){
Product product = new Product(ProductType.Synonym, item.getId());
product.setCount(synonyms.length);
product.setCount(synonyms.size());
item.setProducts(Collections.singletonList(product));
}
Vernacular[] vernaculars = binding.getAphiaVernacularsByID(record.getAphiaID());
Collection<Vernacular> vernaculars = wormsClient.aphiaVernacularsByAphiaId(record.aphiaId);
if (vernaculars!=null){
// logger.debug("found vernacular name");
for (Vernacular vernacular : vernaculars) {
if (vernacular.getLanguage_code()!=null){
CommonName a = new CommonName(vernacular.getLanguage(),vernacular.getVernacular());
if (vernacular.languageCode!=null){
CommonName a = new CommonName(vernacular.language,vernacular.vernacular);
listCommNames.add(a);
}
}
}
item.setScientificNameAuthorship(record.getAuthority());
item.setLsid(record.getLsid());
item.setScientificNameAuthorship(record.authority);
item.setLsid(record.lsid);
item.setCitation(record.getCitation());
item.setCitation(record.citation);
item.setCredits(Utils.createCredits());
item.setCommonNames(listCommNames);
item.setDataSet(ds);
if (record.getRank()!=null)
item.setRank(record.getRank());
else if (record.getScientificname().equals("Biota"))
if (record.taxonomicRank!=null)
item.setRank(record.taxonomicRank);
else if (record.scientificName.equals("Biota"))
item.setRank("Superdomain");
item.setParent(Utils.retrieveTaxon(binding.getAphiaClassificationByID(record.getAphiaID()), record.getAphiaID()));
item.setParent(Utils.retrieveTaxon(wormsClient.aphiaClassificationByAphiaId(record.aphiaId), record.aphiaId));
if (writer.isAlive())
writer.write(item);
else
@ -180,9 +170,9 @@ public class WormsPlugin extends AbstractPlugin {
}
}
offset+=offsetlimit;
} while (records!=null && records.length==offsetlimit);
} while (records!=null && records.size()==offsetlimit);
} catch (RemoteException e) {
} catch (WormsClientException e) {
logger.error("error contacting WoRMS service", e);
throw new ExternalRepositoryException(e);
} catch (Throwable e) {

93
src/main/java/org/gcube/data/spd/wormsplugin/capabilities/ClassificationCapabilityImpl.java
View File

@ -2,6 +2,7 @@ package org.gcube.data.spd.wormsplugin.capabilities;
import java.rmi.RemoteException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
@ -26,9 +27,11 @@ import org.gcube.data.spd.wormsplugin.WormsPlugin;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import aphia.v1_0.worms.AphiaRecord;
import aphia.v1_0.worms.Source;
import aphia.v1_0.worms.Vernacular;
import de.uni_jena.cs.fusion.client.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.Source;
import de.uni_jena.cs.fusion.client.worms.Vernacular;
import de.uni_jena.cs.fusion.client.worms.WormsClientException;
public class ClassificationCapabilityImpl extends ClassificationCapability {
@ -51,11 +54,11 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
// logger.trace(id);
List<TaxonomyItem> list = new ArrayList<TaxonomyItem>();
try {
AphiaRecord[] records;
Collection<AphiaRecord> records;
final int offsetlimit=50;
int offset =1;
do{
records = WormsPlugin.binding.getAphiaChildrenByID(Integer.parseInt(id), offset);
records = WormsPlugin.wormsClient.aphiaChildrenByAphiaId(Long.parseLong(id), false, offset);
if (records!=null){
// logger.debug(records.length);
@ -66,7 +69,7 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
}
}
offset+=offsetlimit;
} while (records!=null && records.length==offsetlimit);
} while (records!=null && records.size()==offsetlimit);
}catch (NumberFormatException e) {
logger.error("id not valid",e);
throw new IdNotValidException(e);
@ -81,20 +84,20 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
public void retrieveTaxa(ObjectWriter<TaxonomyItem> writer, String word, RecordType type) throws ExternalRepositoryException{
Set<Integer> hash = new HashSet<Integer>();
Set<Long> hash = new HashSet<Long>();
try {
AphiaRecord[] records = null;
Collection<AphiaRecord> records = null;
final int offsetlimit=50;
int offset =1;
do{
switch (type) {
case SCIENTIFIC:
records = WormsPlugin.binding.getAphiaRecords(word, true, false, false, offset);
records = WormsPlugin.wormsClient.aphiaRecordsByName(word, true, false, offset);
break;
case VERNACULAR:
records = WormsPlugin.binding.getAphiaRecordsByVernacular(word, true, offset);
records = WormsPlugin.wormsClient.aphiaRecordsByVernacular(word, true, offset);
break;
default:
logger.warn("invalid record type");
@ -104,11 +107,11 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
if (records!=null){
for (AphiaRecord record : records){
if (hash.contains(record.getAphiaID())){
if (hash.contains(record.aphiaId)){
continue;
}
hash.add(record.getAphiaID());
hash.add(record.aphiaId);
TaxonomyItem item = createItem(record, true);
if ((item != null) && (writer.isAlive()))
@ -120,7 +123,7 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
offset+=offsetlimit;
} while (records!=null && records.length==offsetlimit);
} while (records!=null && records.size()==offsetlimit);
} catch (Throwable e) {
logger.error("error contacting worms service", e);
@ -130,33 +133,33 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
}
//create TaxonomyItem
private TaxonomyItem createItem(AphiaRecord record, Boolean flag) throws RemoteException {
private TaxonomyItem createItem(AphiaRecord record, Boolean flag) throws WormsClientException {
TaxonomyItem item = null;
String scientificname = record.getScientificname();
String scientificname = record.scientificName;
// logger.trace("scientificname " + scientificname);
if (scientificname != null ){
item = new TaxonomyItem(record.getAphiaID()+"");
item = new TaxonomyItem(record.aphiaId+"");
item.setScientificName(record.getScientificname());
item.setScientificNameAuthorship(record.getAuthority());
item.setLsid(record.getLsid());
item.setScientificName(record.scientificName);
item.setScientificNameAuthorship(record.authority);
item.setLsid(record.lsid);
item.setCredits(Utils.createCredits());
item.setCitation(record.getCitation());
item.setCitation(record.citation);
if (record.getRank()!=null)
item.setRank(record.getRank());
else if (record.getScientificname().equals("Biota"))
if (record.taxonomicRank!=null)
item.setRank(record.taxonomicRank);
else if (record.scientificName.equals("Biota"))
item.setRank("Superdomain");
List<CommonName> listCommNames = new ArrayList<CommonName> ();
Vernacular[] vernaculars = WormsPlugin.binding.getAphiaVernacularsByID(record.getAphiaID());
Collection<Vernacular> vernaculars = WormsPlugin.wormsClient.aphiaVernacularsByAphiaId(record.aphiaId);
if (vernaculars!=null){
for (Vernacular vernacular : vernaculars) {
if (vernacular.getLanguage_code()!=null){
CommonName a = new CommonName(vernacular.getLanguage(),vernacular.getVernacular());
if (vernacular.languageCode!=null){
CommonName a = new CommonName(vernacular.language,vernacular.vernacular);
listCommNames.add(a);
}
}
@ -164,20 +167,20 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
item.setCommonNames(listCommNames);
try{
if (record.getStatus().equals("accepted"))
if (record.status.equals("accepted"))
item.setStatus(new TaxonomyStatus("accepted", Status.ACCEPTED));
else if (record.getStatus().equals("unaccepted") && WormsPlugin.binding.getAphiaRecordByID(record.getValid_AphiaID()).getStatus().equals("accepted")){
else if (record.status.equals("unaccepted") && WormsPlugin.wormsClient.aphiaRecordByAphiaId(record.validAphiaId).status.equals("accepted")){
// logger.trace(WormsPlugin.binding.getAphiaSynonymsByID(record.getValid_AphiaID()));
item.setStatus(new TaxonomyStatus(Status.SYNONYM, record.getValid_AphiaID()+"", "synonym"));}
item.setStatus(new TaxonomyStatus(Status.SYNONYM, record.validAphiaId+"", "synonym"));}
else
item.setStatus(new TaxonomyStatus(record.getStatus(), Status.UNKNOWN));
item.setStatus(new TaxonomyStatus(record.status, Status.UNKNOWN));
}catch (Exception e) {
item.setStatus(new TaxonomyStatus(record.getStatus(), Status.UNKNOWN));
item.setStatus(new TaxonomyStatus(record.status, Status.UNKNOWN));
}
if (flag){
try{
item.setParent(Utils.retrieveTaxonomy( WormsPlugin.binding.getAphiaClassificationByID(record.getAphiaID()), record.getAphiaID()));
item.setParent(Utils.retrieveTaxonomy( WormsPlugin.wormsClient.aphiaClassificationByAphiaId(record.aphiaId), record.aphiaId));
}catch (Exception e) {
item.setParent(null);
}
@ -185,25 +188,25 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
else
item.setParent(null);
Source[] sources = null;
if ((sources= WormsPlugin.binding.getSourcesByAphiaID(record.getAphiaID()))!=null){
Collection<Source> sources = null;
if ((sources= WormsPlugin.wormsClient.aphiaSourcesByAphiaId(record.aphiaId))!=null){
for (Source source : sources){
// logger.trace(source.getReference());
if (source==null)
continue;
if (source.getReference()!=null){
if (source.reference!=null){
StringBuilder p = new StringBuilder();
p.append(source.getReference());
if (source.getLink()!=null){
p.append(source.reference);
if (source.link!=null){
p.append(", available online at ");
p.append(source.getLink());
p.append(source.link);
}
if (source.getUrl()!=null){
if (source.url!=null){
p.append(", details: ");
p.append(source.getUrl());
p.append(source.url);
}
ElementProperty property = new ElementProperty(source.getUse(), p.toString());
ElementProperty property = new ElementProperty(source.use, p.toString());
item.addProperty(property);
}
}
@ -250,14 +253,14 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
AphiaRecord record = null;
try {
record = WormsPlugin.binding.getAphiaRecordByID(Integer.parseInt(id));
record = WormsPlugin.wormsClient.aphiaRecordByAphiaId(Long.parseLong(id));
if (record!=null){
tax = createItem(record, true);
}
} catch (NumberFormatException e) {
logger.error("NumberFormatException", e);
throw new IdNotValidException(e);
} catch (RemoteException e) {
} catch (WormsClientException e) {
logger.error("Remote Error", e);
throw new ExternalRepositoryException(e);
}
@ -272,8 +275,8 @@ public class ClassificationCapabilityImpl extends ClassificationCapability {
throws IdNotValidException, MethodNotSupportedException, ExternalRepositoryException {
try{
AphiaRecord[] records = null;
if ((records = WormsPlugin.binding.getAphiaSynonymsByID(Integer.parseInt(id)))!=null){
Collection<AphiaRecord> records = null;
if ((records = WormsPlugin.wormsClient.aphiaSynonymsByAphiaId(Long.parseLong(id)))!=null){
for (AphiaRecord record : records){
TaxonomyItem tax = createItem(record, true);

22
src/main/java/org/gcube/data/spd/wormsplugin/capabilities/ExpansionCapabilityImpl.java
View File

@ -1,6 +1,6 @@
package org.gcube.data.spd.wormsplugin.capabilities;
import java.rmi.RemoteException;
import java.util.Collection;
import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
import org.gcube.data.spd.model.exceptions.StreamNonBlockingException;
@ -10,7 +10,8 @@ import org.gcube.data.spd.wormsplugin.WormsPlugin;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import aphia.v1_0.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.WormsClientException;
public class ExpansionCapabilityImpl implements ExpansionCapability {
@ -22,32 +23,33 @@ public class ExpansionCapabilityImpl implements ExpansionCapability {
logger.debug("searching synonyms for "+scientifcName);
int offset =1;
int elements =20;
AphiaRecord[] records = null;
Collection<AphiaRecord> records = null;
do{
try{
records = WormsPlugin.binding.getAphiaRecords(scientifcName, true, false, false, offset);
records = WormsPlugin.wormsClient.aphiaRecordsByName(scientifcName, true, false, offset);
if (records!=null){
for (AphiaRecord record : records){
try{
AphiaRecord[] synonyms = WormsPlugin.binding.getAphiaSynonymsByID(record.getAphiaID());
Collection<AphiaRecord> synonyms = WormsPlugin.wormsClient.aphiaSynonymsByAphiaId(record.aphiaId);
if (synonyms!=null){
for (AphiaRecord synonym: synonyms){
if (!writer.isAlive()) return;
writer.write(synonym.getScientificname());
logger.debug("found synonym "+synonym.getScientificname());
writer.write(synonym.scientificName);
logger.debug("found synonym "+synonym.scientificName);
}
}
}catch (Exception e) {
writer.write(new StreamNonBlockingException("WoRMS",scientifcName));
logger.error("error retrieving synonyms for aphia id "+record.getAphiaID(), e);
logger.error("error retrieving synonyms for aphia id "+record.aphiaId, e);
}
}
}
} catch (RemoteException e) {
} catch (WormsClientException e) {
throw new ExternalRepositoryException(e);
}
offset = elements+offset;
}while(records!=null && records.length == offset );
}while(records!=null && records.size() == offset );
}
}

21
src/main/java/org/gcube/data/spd/wormsplugin/capabilities/NamesMappingImpl.java
View File

@ -1,6 +1,6 @@
package org.gcube.data.spd.wormsplugin.capabilities;
import java.rmi.RemoteException;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
@ -11,7 +11,8 @@ import org.gcube.data.spd.wormsplugin.WormsPlugin;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import aphia.v1_0.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.AphiaRecord;
import de.uni_jena.cs.fusion.client.worms.WormsClientException;
public class NamesMappingImpl implements MappingCapability{
@ -23,26 +24,26 @@ public class NamesMappingImpl implements MappingCapability{
String commonName) throws ExternalRepositoryException{
try {
logger.debug("retrieving mapping for "+commonName);
AphiaRecord[] records;
Collection<AphiaRecord> records;
final int offsetlimit=50;
int offset =1;
Set<String> snSet = new HashSet<String>();
do{
records = WormsPlugin.binding.getAphiaRecordsByVernacular(commonName, true, offset);
records = WormsPlugin.wormsClient.aphiaRecordsByVernacular(commonName, true, offset);
if (records!=null){
for (AphiaRecord record : records){
if (!writer.isAlive()) return;
if (!snSet.contains(record.getScientificname())){
logger.trace("writing (COMMONNAMESMAPPING) "+record.getScientificname() );
writer.write(record.getScientificname());
snSet.add(record.getScientificname());
if (!snSet.contains(record.scientificName)){
logger.trace("writing (COMMONNAMESMAPPING) "+record.scientificName );
writer.write(record.scientificName);
snSet.add(record.scientificName);
}
}
}
offset+=offsetlimit;
} while (records!=null && records.length==offsetlimit);
} while (records!=null && records.size()==offsetlimit);
} catch (RemoteException e) {
} catch (WormsClientException e) {
throw new ExternalRepositoryException(e);
}
}

4
src/test/java/org/gcube/data/spd/wormsplugin/Test.java
View File

@ -1,9 +1,9 @@
package org.gcube.data.spd.wormsplugin;
import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.util.List;
import javax.xml.rpc.ServiceException;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.scope.api.ScopeProvider;
@ -22,7 +22,7 @@ public class Test {
* @throws ServiceException
* @throws ExternalRepositoryException
*/
public static void main(String[] args) throws ServiceException, ExternalRepositoryException {
public static void main(String[] args) throws ExternalRepositoryException {
SimpleQuery query = queryFor(ServiceEndpoint.class);

7
src/test/java/org/gcube/data/spd/wormsplugin/TestExpansionCapability.java
View File

@ -5,7 +5,6 @@ import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.util.List;
import javax.xml.rpc.ServiceException;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.scope.api.ScopeProvider;
@ -23,7 +22,7 @@ public class TestExpansionCapability {
* @throws ServiceException
* @throws ExternalRepositoryException
*/
public static void main(String[] args) throws ServiceException, ExternalRepositoryException {
public static void main(String[] args) throws ExternalRepositoryException {
SimpleQuery query = queryFor(ServiceEndpoint.class);
query.addCondition("$resource/Profile/Category/text() eq 'BiodiversityRepository' and $resource/Profile/Name eq 'WoRMS' ");
@ -44,8 +43,8 @@ public class TestExpansionCapability {
}
}
WormsPlugin.binding = (aphia.v1_0.worms.AphiaNameServiceBindingStub)
new aphia.v1_0.worms.AphiaNameServiceLocator().getAphiaNameServicePort();
/*WormsPlugin.binding = (aphia.v1_0.worms.AphiaNameServiceBindingStub)
new aphia.v1_0.worms.AphiaNameServiceLocator().getAphiaNameServicePort();*/
ExpansionCapabilityImpl b = new ExpansionCapabilityImpl();
b.getSynonyms(new ObjectWriter<String>() {

5
src/test/java/org/gcube/data/spd/wormsplugin/TestMapping.java
View File

@ -3,7 +3,6 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.util.List;
import java.util.Set;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.scope.api.ScopeProvider;
@ -36,8 +35,8 @@ public class TestMapping {
}
}
WormsPlugin.binding = (aphia.v1_0.worms.AphiaNameServiceBindingStub)
new aphia.v1_0.worms.AphiaNameServiceLocator().getAphiaNameServicePort();
/*WormsPlugin.binding = (aphia.v1_0.worms.AphiaNameServiceBindingStub)
new aphia.v1_0.worms.AphiaNameServiceLocator().getAphiaNameServicePort();*/
NamesMappingImpl b = new NamesMappingImpl();