Merge branch '9-accession-api-v1' into 'master'

Resolve "Accession API v1"

Closes #9

See merge request !9

src/main/java/org/genesys2/client/oauth/GenesysApiException.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/org/genesys2/client/oauth/GenesysTokens.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/org/genesys2/client/oauth/HttpConstants.java

+/*
+ * Copyright 2019 Global Crop Diversity Trust
+ *
+ * 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.
+ */
 package org.genesys2.client.oauth;
 
 public class HttpConstants {

src/main/java/org/genesys2/client/oauth/HttpRedirectException.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/org/genesys2/client/oauth/OAuthAuthenticationException.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/org/genesys2/client/oauth/PleaseRetryException.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/org/genesys2/client/oauth/api/GenesysApi.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

src/main/java/org/genesys2/client/oauth/api/accession/AccessionJson.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -32,45 +32,21 @@ public class AccessionJson {
 	private Long genesysId;
 
 	/** The puid. */
-	@JsonProperty(value = Accession.PUID)
-	private String puid;
+	@JsonProperty(value = Accession.DOI)
+	private String doi;
 	
 	/** The inst code. */
 	@JsonProperty(value = Accession.INSTCODE)
-	private String instCode;
+	private String instituteCode;
 
 	/** The acce numb. */
 	@JsonProperty(value = Accession.ACCENUMB)
-	private String acceNumb;
+	private String accessionNumber;
 
 	/** The new acce numb. */
 	@JsonProperty(value = Accession.ACCENUMB_NEW)
 	private String newAcceNumb;
 
-	/** The genus. */
-	@JsonProperty(value = Accession.GENUS)
-	private String genus;
-
-	/** The new genus. */
-	@JsonProperty(value = Accession.GENUS_NEW)
-	private String newGenus;
-
-	/** The species. */
-	@JsonProperty(value = Accession.SPECIES)
-	private String species;
-
-	/** The spauthor. */
-	@JsonProperty(value = Accession.SPAUTHOR)
-	private String spauthor;
-
-	/** The subtaxa. */
-	@JsonProperty(value = Accession.SUBTAXA)
-	private String subtaxa;
-
-	/** The subtauthor. */
-	@JsonProperty(value = Accession.SUBTAUTHOR)
-	private String subtauthor;
-
 	/** The uuid. */
 	@JsonProperty(value = Accession.UUID)
 	private String uuid;
@@ -81,7 +57,7 @@ public class AccessionJson {
 
 	/** The acq date. */
 	@JsonProperty(value = Accession.ACQDATE)
-	private String acqDate;
+	private String acquisitionDate;
 
 	/** The mls stat. */
 	@JsonProperty(value = Accession.MLSSTAT)
@@ -109,7 +85,11 @@ public class AccessionJson {
 
 	/** The bred code. */
 	@JsonProperty(value = Accession.BREDCODE)
-	private String[] bredCode;
+	private String[] breederCode;
+
+	/** The bred code. */
+	@JsonProperty(value = Accession.BREDNAME)
+	private String[] breederName;
 
 	/** The ancest. */
 	@JsonProperty(value = Accession.ANCEST)
@@ -135,6 +115,10 @@ public class AccessionJson {
 	@JsonProperty(value = Accession.GEO)
 	private GeoJson geo;
 
+	/** The taxonomy. */
+	@JsonProperty(value = Accession.TAXONOMY)
+	private TaxonomyJson taxonomy;
+
 	/** The remarks. */
 	@JsonProperty(value = Accession.REMARKS)
 	private Remark[] remarks;
@@ -162,6 +146,7 @@ public class AccessionJson {
 	public AccessionJson() {
 		this.geo = new GeoJson();
 		this.coll = new CollectingJson();
+		this.taxonomy = new TaxonomyJson();
 	}
 
 	/**
@@ -205,56 +190,49 @@ public class AccessionJson {
 	 * @return the puid
 	 */
 	public String getPuid() {
-		return puid;
+		return doi;
 	}
 
 	/**
-	 * @param puid the puid to set
-	 */
-	public void setPuid(String puid) {
-		this.puid = puid;
-	}
-
-	/**
-	 * Gets the inst code.
+	 * Gets the FAO WIEWS institute code.
 	 *
 	 * @return the inst code
 	 */
-	public String getInstCode() {
-		return instCode;
+	public String getInstituteCode() {
+		return instituteCode;
 	}
 
 	/**
 	 * Sets the inst code.
 	 *
-	 * @param instCode the new inst code
+	 * @param instituteCode the new inst code
 	 */
-	public void setInstCode(final String instCode) {
-		this.instCode = instCode;
+	public void setInstituteCode(final String instituteCode) {
+		this.instituteCode = instituteCode;
 	}
 
 	/**
-	 * Gets the acce numb.
+	 * Gets the accession number.
 	 *
-	 * @return the acce numb
+	 * @return the accession number
 	 */
-	public String getAcceNumb() {
-		return acceNumb;
+	public String getAccessionNumber() {
+		return accessionNumber;
 	}
-
+	
 	/**
-	 * Sets the acce numb.
+	 * Sets the accession number.
 	 *
-	 * @param acceNumb the new acce numb
+	 * @param accessionNumber the new accession number
 	 */
-	public void setAcceNumb(final String acceNumb) {
-		this.acceNumb = acceNumb;
+	public void setAccessionNumber(String accessionNumber) {
+		this.accessionNumber = accessionNumber;
 	}
-
+	
 	/**
-	 * Gets the new acce numb.
+	 * Gets the new accession number.
 	 *
-	 * @return the new acce numb
+	 * @return the new accession number
 	 */
 	public String getNewAcceNumb() {
 		return newAcceNumb;
@@ -269,114 +247,6 @@ public class AccessionJson {
 		this.newAcceNumb = newAcceNumb;
 	}
 
-	/**
-	 * Gets the genus.
-	 *
-	 * @return the genus
-	 */
-	public String getGenus() {
-		return genus;
-	}
-
-	/**
-	 * Sets the genus.
-	 *
-	 * @param genus the new genus
-	 */
-	public void setGenus(final String genus) {
-		this.genus = genus;
-	}
-
-	/**
-	 * Gets the new genus.
-	 *
-	 * @return the new genus
-	 */
-	public String getNewGenus() {
-		return newGenus;
-	}
-
-	/**
-	 * Sets the new genus.
-	 *
-	 * @param newGenus the new new genus
-	 */
-	public void setNewGenus(final String newGenus) {
-		this.newGenus = newGenus;
-	}
-
-	/**
-	 * Gets the species.
-	 *
-	 * @return the species
-	 */
-	public String getSpecies() {
-		return species;
-	}
-
-	/**
-	 * Sets the species.
-	 *
-	 * @param species the new species
-	 */
-	public void setSpecies(final String species) {
-		this.species = species;
-	}
-
-	/**
-	 * Gets the spauthor.
-	 *
-	 * @return the spauthor
-	 */
-	public String getSpauthor() {
-		return spauthor;
-	}
-
-	/**
-	 * Sets the spauthor.
-	 *
-	 * @param spauthor the new spauthor
-	 */
-	public void setSpauthor(final String spauthor) {
-		this.spauthor = spauthor;
-	}
-
-	/**
-	 * Gets the subtaxa.
-	 *
-	 * @return the subtaxa
-	 */
-	public String getSubtaxa() {
-		return subtaxa;
-	}
-
-	/**
-	 * Sets the subtaxa.
-	 *
-	 * @param subtaxa the new subtaxa
-	 */
-	public void setSubtaxa(final String subtaxa) {
-		this.subtaxa = subtaxa;
-	}
-
-	/**
-	 * Gets the subtauthor.
-	 *
-	 * @return the subtauthor
-	 */
-	public String getSubtauthor() {
-		return subtauthor;
-	}
-
-	/**
-	 * Sets the subtauthor.
-	 *
-	 * @param subtauthor the new subtauthor
-	 */
-	public void setSubtauthor(final String subtauthor) {
-		this.subtauthor = subtauthor;
-	}
-
 	/**
 	 * Gets the uuid.
 	 *
@@ -414,21 +284,21 @@ public class AccessionJson {
 	}
 
 	/**
-	 * Gets the acq date.
+	 * Gets the acquisition date.
 	 *
-	 * @return the acq date
+	 * @return the acquisition date
 	 */
-	public String getAcqDate() {
-		return acqDate;
+	public String getAcquisitionDate() {
+		return acquisitionDate;
 	}
-
+	
 	/**
-	 * Sets the acq date.
+	 * Sets the acquisition date.
 	 *
-	 * @param acqDate the new acq date
+	 * @param acquisitionDate the new acquisition date
 	 */
-	public void setAcqDate(final String acqDate) {
-		this.acqDate = acqDate;
+	public void setAcquisitionDate(String acquisitionDate) {
+		this.acquisitionDate = acquisitionDate;
 	}
 
 	/**
@@ -545,7 +415,7 @@ public class AccessionJson {
 	 * @return the bred code
 	 */
 	public String[] getBredCode() {
-		return bredCode;
+		return breederCode;
 	}
 
 	/**
@@ -554,7 +424,7 @@ public class AccessionJson {
 	 * @param bredCode the new bred code
 	 */
 	public void setBredCode(final String[] bredCode) {
-		this.bredCode = bredCode;
+		this.breederCode = bredCode;
 	}
 
 	/**
@@ -665,6 +535,24 @@ public class AccessionJson {
 		this.geo = geo;
 	}
 
+	/**
+	 * Gets the taxonomy.
+	 *
+	 * @return the taxonomy
+	 */
+	public TaxonomyJson getTaxonomy() {
+		return taxonomy;
+	}
+
+	/**
+	 * Sets the taxonomy.
+	 *
+	 * @param taxonomy the new taxonomy
+	 */
+	public void setTaxonomy(final TaxonomyJson taxonomy) {
+		this.taxonomy = taxonomy;
+	}
+
 	/**
 	 * Gets the remarks.
 	 *

src/main/java/org/genesys2/client/oauth/api/accession/Api1Constants.java

 /*
- * Copyright 2016 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -40,69 +40,52 @@ public interface Api1Constants {
 		/**
 		 * WIEWS code of accession holding institute.
 		 */
-		public static final String INSTCODE = "instCode";
+		public static final String INSTCODE = "instituteCode";
 
 		/**
 		 * Accession number.
 		 */
-		public static final String ACCENUMB = "acceNumb";
-
-		/** Used to assign new ACCENUMB. */
-		public static final String ACCENUMB_NEW = "newAcceNumb";
+		public static final String ACCENUMB = "accessionNumber";
 
 		/**
-		 * Reported genus of accession.
+		 * Used to assign new ACCENUMB
 		 */
-		public static final String GENUS = "genus";
-
-		/**
-		 * May be used to assign a different genus.
-		 */
-		public static final String GENUS_NEW = "newGenus";
-
-		/**
-		 * Specific epithet portion of the scientific name, in latin, in lowercase letters.
-		 * Following abbreviation is allowed: ‘sp.’
-		 */
-		public static final String SPECIES = "species";
-
-		/** Corresponds to MCPD SPAUTHOR. */
-		public static final String SPAUTHOR = "spauthor";
-
-		/** Corresponds to MCPD SUBTAXA. */
-		public static final String SUBTAXA = "subtaxa";
-
-		/** Corresponds to MCPD SUBTAUTHOR. */
-		public static final String SUBTAUTHOR = "subtauthor";
+		public static final String ACCENUMB_NEW = "newAcceNumb";
 
 		/**
-		 * Universally Unique IDentifier for the accession, assigned by the first holding institute
-		 * and immutable when accession is duplicated in another institute.
+		 * Universally Unique IDentifier for the accession, assigned by the
+		 * first holding institute and immutable when accession is duplicated in
+		 * another institute.
 		 */
 		public static final String UUID = "uuid";
 
 		/**
 		 * ISO3 country code of country of origin.
 		 */
-		public static final String ORIGCTY = "orgCty";
+		public static final String ORIGCTY = "origCty";
 
 		/**
-		 * Date on which the accession entered the collection as YYYYMMDD. Missing data (MM or DD)
-		 * should be indicated with hyphens. Leading zeros are required.
+		 * Date on which the accession entered the collection as YYYYMMDD.
+		 * Missing data (MM or DD) should be indicated with hyphens. Leading
+		 * zeros are required.
 		 */
-		public static final String ACQDATE = "acqDate";
+		public static final String ACQDATE = "acquisitionDate";
 
 		/**
-		 * The status of an accession with regards to the Multilateral System (MLS) of the
-		 * International Treaty on PlantGenetic Resources for Food and Agriculture.
+		 * The status of an accession with regards to the Multilateral System
+		 * (MLS) of the International Treaty on PlantGenetic Resources for Food
+		 * and Agriculture.
 		 */
-		public static final String MLSSTAT = "mlsStat";
+		public static final String MLSSTAT = "mlsStatus";
 
-		/** Is the accession “FAO In trust”. */
+		/**
+		 * Is the accession “FAO In trust”
+		 */
 		public static final String INTRUST = "inTrust";
 
 		/**
-		 * The general availability of the accession for distribution, but subject to current stock.
+		 * The general availability of the accession for distribution, but
+		 * subject to current stock.
 		 */
 		public static final String AVAILABLE = "available";
 
@@ -111,26 +94,30 @@ public interface Api1Constants {
 		 */
 		public static final String STORAGE = "storage";
 
-		/** MCPD Sample status. */
+		/**
+		 * MCPD Sample status
+		 */
 		public static final String SAMPSTAT = "sampStat";
 
 		/**
-		 * FAO Institute Code (WIEWS code) of the institute where a safety duplicate of the
-		 * accession is maintained.
+		 * FAO Institute Code (WIEWS code) of the institute where a safety
+		 * duplicate of the accession is maintained.
 		 */
 		public static final String DUPLSITE = "duplSite";
 
 		/**
 		 * Corresponds to BREDCODE.
 		 */
-		public static final String BREDCODE = "bredCode";
+		public static final String BREDCODE = "breederCode";
 
 		/**
 		 * Corresponds to ANCEST.
 		 */
 		public static final String ANCEST = "ancest";
 
-		/** FAO WIEWS code of the donor institute. */
+		/**
+		 * FAO WIEWS code of the donor institute
+		 */
 		public static final String DONORCODE = "donorCode";
 
 		/**
@@ -139,58 +126,125 @@ public interface Api1Constants {
 		public static final String DONORNUMB = "donorNumb";
 
 		/**
-		 * Name of the donor institute (or person). Provide only when donorCode is not available.
+		 * Name of the donor institute (or person). Provide only when donorCode
+		 * is not available.
 		 */
 		public static final String DONORNAME = "donorName";
 
-		/** Object containing the collecting data. */
+		/**
+		 * Object containing the collecting data
+		 */
 		public static final String COLL = "coll";
 
-		/** Object containing georeference data. */
+		/**
+		 * Object containing georeference data
+		 */
 		public static final String GEO = "geo";
 
-		/** MCPD Remarks. */
+		/** 
+		 * Object containing taxonomy data.
+		 * */
+		public static final String TAXONOMY = "taxonomy";
+
+		/**
+		 * MCPD Remarks
+		 */
 		public static final String REMARKS = "remarks";
 
 		/**
-		 * Marks if accession record is about a historic holding and the accession no longer exists.
+		 * Marks if accession record is about a historic holding and the
+		 * accession no longer exists.
 		 */
 		public static final String HISTORIC = "historic";
 
-		/** Accession name. */
+		/**
+		 * Accession name
+		 */
 		public static final String ACCENAME = "acceName";
 
-		/** Other numbers. */
+		/**
+		 * Other numbers
+		 */
 		public static final String OTHERNUMB = "otherNumb";
 
 		/**
-		 * URL linking to additional data about the accession either in the holding genebank or from
-		 * another source.
+		 * URL linking to additional data about the accession either in the
+		 * holding genebank or from another source.
 		 */
 		public static final String ACCEURL = "acceUrl";
 
-