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Commit ca9c6a5d authored by Ray Liu's avatar Ray Liu
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src/FileProcessor.java → src/biotree/FileProcessor.java
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View file @ ca9c6a5d
package biotree;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
......
src/record/Record.java → src/biotree/Record.java
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− 1
View file @ ca9c6a5d
package record;
package biotree;
public class Record {
private final int eventId;
......
src/biotree/Species.java deleted 100644 → 0
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− 41
View file @ 58622f20
package biotree;
public class Species {
private final String species;
private final String bClass;
private final String order;
private final String family;
private final String genus;
public Species(String bClass, String order, String family, String genus, String species) {
this.species = species;
this.bClass = bClass;
this.order = order;
this.family = family;
this.genus = genus;
}
public String getSpecies() {
return this.species;
}
public String getBClass() {
return this.bClass;
}
public String getOrder() {
return this.order;
}
public String getFamily() {
return this.family;
}
public String getGenus() {
return this.genus;
}
public String toString() {
return bClass + " " + order + " " + family + " " + genus + " " + species;
}
}
src/biotree/TaxonNode.java 0 → 100644
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− 0
View file @ ca9c6a5d
package biotree;
public class TaxonNode {
}
src/record/TaxonType.java → src/biotree/TaxonType.java
+ 11
− 11
View file @ ca9c6a5d
package record;
/**
* Enumeration of classifications of Taxa.
* @author Christopher W. Schankula
*
*/
public enum TaxonType {
KINGDOM, PHYLUM, CLASS, ORDER,
FAMILY, GENUS, SPECIES, SUBSPECIES;
}
package biotree;
/**
* Enumeration of classifications of Taxa.
* @author Christopher W. Schankula
*
*/
public enum TaxonType {
KINGDOM, PHYLUM, CLASS, ORDER,
FAMILY, GENUS, SPECIES, SUBSPECIES;
}
src/biotree/WormsAPI.java
+ 99
− 100
View file @ ca9c6a5d
package biotree;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import record.TaxonType;
import tuple.Tuple;
public class WormsAPI {
public static void main(String[] args) throws IOException {
//small test
System.out.println(nameToID("Neogobius melanostomus"));
}
/**
* Search the WORMS database by scientific name to return Aphia (taxon) ID.
* This must be an exact name or it will fail. Use fuzzyNameToID if the name
* is not exact.
* @param scientificName Scientific name of taxon (family, genus, species, etc)
* @return Aphia (taxon) ID of given scientific name.
* @throws IOException
*/
public static int nameToID(String scientificName) throws IOException{
scientificName = repSpaces(scientificName);
String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaIDByName/%s?marine_only=false", scientificName));
return Integer.parseInt(resp);
}
/**
* Search the WORMS database by fuzzy scientific name (a slightly misspelled name).
* This has the advantage of being more flexible but it can be less accurate and it
* is slower. If you have the actual scientific name, use nameToID() instead.
* @param fuzzyName Fuzzy scientific name of taxon (family, genus, species, etc)
* @return Aphia (taxon) ID of given scientific name.
* @throws IOException
*/
public static int fuzzyNameToID(String fuzzyName) throws IOException{
fuzzyName = repSpaces(fuzzyName);
String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%5B%5D=%s&marine_only=true", fuzzyName));
//TODO: finish this function.
return 123123;
}
/**
* Search by taxonId (AphiaID) and return bioclassification of that and above.
* http://marinespecies.org/rest/
* /AphiaClassificationByAphiaID/{ID}
*/
public static Tuple<TaxonType,Integer>[] idToClassification(int taxonId) {
return null;
}
/**
* Perform a GET request to the given URL and return the content of the response.
* @param url The URL to which to make a request.
* @return The content returned by the server (if successful).
* @throws IOException
*/
private static String makeRequest(String url) throws IOException {
//Request method adapted from http://www.baeldung.com/java-http-request
//create new URL instance
URL urll = new URL(url);
//create and set up connection
HttpURLConnection con = (HttpURLConnection) urll.openConnection();
con.setRequestMethod("GET");
int status = con.getResponseCode();
BufferedReader in = new BufferedReader(
new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer content = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
content.append(inputLine);
}
in.close();
con.disconnect();
return content.toString();
}
/**
* Helper to replace a space with the correct one for URLs.
* @param in Input string
* @return String with spaces replaced by "%20" for spaces in URLs.
*/
private static String repSpaces(String in) {
return in.replaceAll(" ", "%20");
}
}
package biotree;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import tuple.Tuple;
public class WormsAPI {
public static void main(String[] args) throws IOException {
//small test
System.out.println(nameToID("Neogobius melanostomus"));
}
/**
* Search the WORMS database by scientific name to return Aphia (taxon) ID.
* This must be an exact name or it will fail. Use fuzzyNameToID if the name
* is not exact.
* @param scientificName Scientific name of taxon (family, genus, species, etc)
* @return Aphia (taxon) ID of given scientific name.
* @throws IOException
*/
public static int nameToID(String scientificName) throws IOException{
scientificName = repSpaces(scientificName);
String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaIDByName/%s?marine_only=false", scientificName));
return Integer.parseInt(resp);
}
/**
* Search the WORMS database by fuzzy scientific name (a slightly misspelled name).
* This has the advantage of being more flexible but it can be less accurate and it
* is slower. If you have the actual scientific name, use nameToID() instead.
* @param fuzzyName Fuzzy scientific name of taxon (family, genus, species, etc)
* @return Aphia (taxon) ID of given scientific name.
* @throws IOException
*/
public static int fuzzyNameToID(String fuzzyName) throws IOException{
fuzzyName = repSpaces(fuzzyName);
String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%5B%5D=%s&marine_only=true", fuzzyName));
//TODO: finish this function.
return 123123;
}
/**
* Search by taxonId (AphiaID) and return bioclassification of that and above.
* http://marinespecies.org/rest/
* /AphiaClassificationByAphiaID/{ID}
*/
public static Tuple<TaxonType,Integer>[] idToClassification(int taxonId) {
return null;
}
/**
* Perform a GET request to the given URL and return the content of the response.
* @param url The URL to which to make a request.
* @return The content returned by the server (if successful).
* @throws IOException
*/
private static String makeRequest(String url) throws IOException {
//Request method adapted from http://www.baeldung.com/java-http-request
//create new URL instance
URL urll = new URL(url);
//create and set up connection
HttpURLConnection con = (HttpURLConnection) urll.openConnection();
con.setRequestMethod("GET");
int status = con.getResponseCode();
BufferedReader in = new BufferedReader(
new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer content = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
content.append(inputLine);
}
in.close();
con.disconnect();
return content.toString();
}
/**
* Helper to replace a space with the correct one for URLs.
* @param in Input string
* @return String with spaces replaced by "%20" for spaces in URLs.
*/
private static String repSpaces(String in) {
return in.replaceAll(" ", "%20");
}
}
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