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Merge pull request #47 from charvolant/master
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Release 1.4.8
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@charvolant
charvolant authored Mar 23, 2023
2 parents 014eb1a + 31f0509 commit 53d2158
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Showing 4 changed files with 80 additions and 29 deletions.
4 changes: 2 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>au.org.ala</groupId>
<artifactId>sds</artifactId>
<version>1.4.7</version>
<version>1.4.8</version>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/AtlasOfLivingAustralia/sds/issues</url>
Expand Down Expand Up @@ -56,7 +56,7 @@
<dependency>
<groupId>au.org.ala</groupId>
<artifactId>ala-name-matching-search</artifactId>
<version>4.2</version>
<version>4.3</version>
<scope>compile</scope>
</dependency>
<dependency>
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32 changes: 27 additions & 5 deletions src/main/java/au/org/ala/sds/model/SDSSpeciesListItemDTO.java
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Expand Up @@ -15,6 +15,7 @@
package au.org.ala.sds.model;

import com.google.common.collect.Lists;
import org.codehaus.jackson.annotate.JsonIgnore;

import java.util.List;
import java.util.Map;
Expand All @@ -31,6 +32,7 @@ public class SDSSpeciesListItemDTO {
private String dataResourceUid;
private List<Map<String, String>> kvpValues;
public static final List<String> commonNameLabels= Lists.newArrayList("commonname","vernacularname");
private String commonName;

public String getGuid() {
return guid;
Expand All @@ -40,6 +42,19 @@ public void setGuid(String guid) {
this.guid = guid;
}

public String getCommonName() {
return commonName;
}

public void setCommonName(String commonName) {
this.commonName = commonName;
}

// Added for the change data structure returned by lists
public void setLsid(String lsid) {
this.guid = lsid;
}

public String getName() {
return name;
}
Expand Down Expand Up @@ -70,28 +85,35 @@ public void setFamily(String family) {

public void setKvpValues(List<Map<String, String>> kvpValues) {
this.kvpValues = kvpValues;

// family has moved to kvpValues
for(Map<String, String> pair: kvpValues){
if("family".equalsIgnoreCase(pair.get("key"))){
setFamily(pair.get("value"));
}
}
}
public String getKVPValue(String key){
for(Map<String, String> pair: kvpValues){
if(key.equals(pair.get("key"))){
if(key.equalsIgnoreCase(pair.get("key").replaceAll("[^a-zA-Z]", ""))){
return pair.get("value");
}
}
return null;
}
public String getKVPValue(List<String> keys){
public String getKVPValueCommonName(){
for(Map<String, String> pair: kvpValues){
if(keys.contains(pair.get("key").toLowerCase().replaceAll(" ", ""))){
if(commonNameLabels.contains(pair.get("key").toLowerCase().replaceAll(" ", ""))){
return pair.get("value");
}
}
return null;
return commonName;
}

@Override
public String toString() {
return "SDSSpeciesListItemDTO{" +
"guid='" + guid + '\'' +
"lsid='" + guid + '\'' +
", name='" + name + '\'' +
", dataResourceUid='" + dataResourceUid + '\'' +
", kvpValues=" + kvpValues +
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/au/org/ala/sds/util/SensitiveSpeciesXmlBuilder.java
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Expand Up @@ -71,7 +71,7 @@ public static boolean generateFromWebservices(OutputStream out, Date lastGenerat
}

//Step 1: get all of the items that have a guid
List<SDSSpeciesListItemDTO> guidItems = SpeciesListUtil.getSDSListItems(true);
List<SDSSpeciesListItemDTO> guidItems = SpeciesListUtil.getSDSListItems(sdsLists.keySet(), true);
if(sdsLists.isEmpty() || guidItems == null || guidItems.isEmpty()) {
return false;
}
Expand Down Expand Up @@ -102,7 +102,7 @@ public static boolean generateFromWebservices(OutputStream out, Date lastGenerat
}
sensitiveSpecies.setAttribute("guid", item.getGuid());
sensitiveSpecies.setAttribute("rank", rank);
String commonName = item.getKVPValue(item.commonNameLabels);
String commonName = item.getKVPValueCommonName();
sensitiveSpecies.setAttribute("commonName", commonName != null ? commonName : "");
doc.getRootElement().addContent(sensitiveSpecies);
currentGuid = item.getGuid();
Expand All @@ -121,7 +121,7 @@ public static boolean generateFromWebservices(OutputStream out, Date lastGenerat
}

//Step 2: get all the items that could NOT be matched to the current species list
List<SDSSpeciesListItemDTO> unmatchedItems = SpeciesListUtil.getSDSListItems(false);
List<SDSSpeciesListItemDTO> unmatchedItems = SpeciesListUtil.getSDSListItems(sdsLists.keySet(), false);
String currentName = "";
sensitiveSpecies = null;
instances = null;
Expand All @@ -143,7 +143,7 @@ public static boolean generateFromWebservices(OutputStream out, Date lastGenerat
logger.error("Unable to get rank for " + item.getName(), e);
}
sensitiveSpecies.setAttribute("rank", rank);
String commonName = item.getKVPValue(item.commonNameLabels);
String commonName = item.getKVPValueCommonName();
sensitiveSpecies.setAttribute("commonName", commonName != null ? commonName : "");
//sensitiveSpecies.setAttribute("commonName", st.getCommonName() != null ? st.getCommonName() : "");
doc.getRootElement().addContent(sensitiveSpecies);
Expand Down
65 changes: 47 additions & 18 deletions src/main/java/au/org/ala/sds/util/SpeciesListUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@

import au.org.ala.sds.model.SDSSpeciesListDTO;
import au.org.ala.sds.model.SDSSpeciesListItemDTO;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.codehaus.jackson.map.DeserializationConfig;
import org.codehaus.jackson.map.ObjectMapper;
Expand All @@ -25,8 +26,7 @@
import java.io.InputStream;
import java.net.URL;
import java.net.URLConnection;
import java.util.List;
import java.util.Map;
import java.util.*;

/**
* Provides utility methods required to interface with the species list tool. Allows the SDS
Expand Down Expand Up @@ -83,21 +83,50 @@ public static Map<String,SDSSpeciesListDTO> getSDSLists(){
* Retrieves the "isSDS" species list items ordering them by guid/scientific name
* @return
*/
public static List<SDSSpeciesListItemDTO> getSDSListItems(boolean hasMatch){
public static List<SDSSpeciesListItemDTO> getSDSListItems(Collection<String> dataResourceUids, boolean hasMatch){
try{
String suffix = hasMatch ? "&guid=isNotNull:guid&sort=guid" : "&guid=isNull:guid&sort=rawScientificName";
URL url = new URL(Configuration.getInstance().getListToolUrl() + "/ws/speciesListItems?isSDS=eq:true" + suffix);
ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationConfig.Feature.FAIL_ON_UNKNOWN_PROPERTIES, false);
URLConnection connection = url.openConnection();
logger.debug("Looking up location using " + url);
InputStream inStream = connection.getInputStream();
String suffix = hasMatch ? "&sort=guid" : "&sort=rawScientificName";
List<SDSSpeciesListItemDTO> values = new ArrayList();

java.util.List<SDSSpeciesListItemDTO> values = mapper.readValue(
inStream,
new TypeReference<List<SDSSpeciesListItemDTO>>(){}
);
logger.debug(values);
String drUids = StringUtils.join(dataResourceUids, ",");
int offset = 0;
int max = 400;
boolean moreRecords = true;
while(moreRecords) {
URL url = new URL(Configuration.getInstance().getListToolUrl() + "/ws/speciesListItems?isSDS=eq:true" + suffix + "&druid=" + drUids + "&includeKVP=true&max=" + max + "&offset=" + offset);
offset += max;

ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationConfig.Feature.FAIL_ON_UNKNOWN_PROPERTIES, false);
URLConnection connection = url.openConnection();
logger.error("Looking up location using " + url);
InputStream inStream = connection.getInputStream();

java.util.List<SDSSpeciesListItemDTO> drValues = mapper.readValue(
inStream,
new TypeReference<List<SDSSpeciesListItemDTO>>() {
}
);

if (!hasMatch) {
// include only records without an LSID
for (SDSSpeciesListItemDTO item : drValues) {
if (item.getGuid() == null) {
values.add(item);
}
}
} else {
// include only records with an LSID
for (SDSSpeciesListItemDTO item : drValues) {
if (item.getGuid() != null) {
values.add(item);
}
}
}

moreRecords = drValues.size() == max;
}
logger.error(values);
return values;
} catch(Exception e){
logger.error("Unable to get the list items. ", e);
Expand All @@ -106,8 +135,8 @@ public static List<SDSSpeciesListItemDTO> getSDSListItems(boolean hasMatch){
}

public static void main(String[] args){
getSDSLists();
getSDSListItems(true);
getSDSListItems(false);
Map<String, SDSSpeciesListDTO> sdsLists = getSDSLists();
getSDSListItems(sdsLists.keySet(), true);
getSDSListItems(sdsLists.keySet(), false);
}
}

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