diff --git a/src/biotree/WormsAPI.java b/src/biotree/WormsAPI.java
index 63f5e26274ed4d829ffe1c06b8cbe1a55983281f..3a9b7fd0716306dfc30bc592e89b9bd36c242deb 100644
--- a/src/biotree/WormsAPI.java
+++ b/src/biotree/WormsAPI.java
@@ -6,124 +6,129 @@ import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
-
//Need to add library
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import org.json.simple.JSONObject;
-
-
-
-
-
public class WormsAPI {
-
+
public static void main(String[] args) throws IOException, ParseException {
- //small test
+ // small test
System.out.println(nameToID("Neogobius melanostomus"));
/*
- TaxonNode[] taxnodes = idToClassification(126916);
+ * TaxonNode[] taxnodes = idToClassification(126916);
+ *
+ * for (int i =0; i < taxnodes.length;i++) {
+ * System.out.println(taxnodes[i].getTaxonId());
+ * System.out.println(taxnodes[i].getTaxonType());
+ * System.out.println(taxnodes[i].getName()); }
+ */
- for (int i =0; i < taxnodes.length;i++) {
- System.out.println(taxnodes[i].getTaxonId());
- System.out.println(taxnodes[i].getTaxonType());
- System.out.println(taxnodes[i].getName());
- }
- */
-
}
-
+
/**
- * 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)
+ * 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{
+ 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));
-
+ 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)
+ * 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{
+ 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.
+ 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.
- *
+ *
* /AphiaClassificationByAphiaID/{ID}
- * @throws IOException
- * @throws ParseException
+ *
+ * @throws IOException
+ * @throws ParseException
*/
public static TaxonNode[] idToClassification(int taxonId) throws IOException, ParseException {
- String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaClassificationByAphiaID/%d", taxonId));
+ String resp = makeRequest(
+ String.format("http://marinespecies.org/rest/AphiaClassificationByAphiaID/%d", taxonId));
JSONParser parser = new JSONParser();
JSONObject json = (JSONObject) parser.parse(resp);
-
- //Assume length of 8 based on number of taxontypes
+
+ // Assume length of 8 based on number of taxontypes
TaxonNode[] taxnodes = new TaxonNode[8];
- int arraysize = parseIdCall(taxnodes,json,0);
+ int arraysize = parseIdCall(taxnodes, json, 0);
TaxonNode[] copiedArray = new TaxonNode[arraysize];
System.arraycopy(taxnodes, 0, copiedArray, 0, arraysize);
-
+
return copiedArray;
-
+
}
-
-
-
+
/**
- * 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.
+ * 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
+ // 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
+ // 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()));
+
+ BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer content = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
- content.append(inputLine);
+ 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
+ *
+ * @param in
+ * Input string
* @return String with spaces replaced by "%20" for spaces in URLs.
*/
private static String repSpaces(String in) {
@@ -131,37 +136,43 @@ public class WormsAPI {
}
/**
- * Parses the json request recursively and also keeping track of the array length
- * @param nodes the TaxonNode array
- * @param current current rank level of JSON file
- * @param n index of where the TaxonNode is being stored at
+ * Parses the json request recursively and also keeping track of the array
+ * length
+ *
+ * @param nodes
+ * the TaxonNode array
+ * @param current
+ * current rank level of JSON file
+ * @param n
+ * index of where the TaxonNode is being stored at
* @return arraysize number of elements added within array
*/
- private static int parseIdCall(TaxonNode[] nodes,JSONObject current,int n) {
+ private static int parseIdCall(TaxonNode[] nodes, JSONObject current, int n) {
boolean checktype = false;
TaxonNode curNode = null;
int arraysize = n;
- //Checks if rank matches the TaxonType Enum
+ // Checks if rank matches the TaxonType Enum
for (TaxonType c : TaxonType.values()) {
-
- if (c.name().equals((String)current.get("rank"))) {
- checktype= true;
- break;
- }
- else checktype = false;
- }
+
+ if (c.name().equals((String) current.get("rank"))) {
+ checktype = true;
+ break;
+ } else
+ checktype = false;
+ }
JSONObject child = (JSONObject) current.get("child");
-
+
if (checktype == true) {
- curNode = new TaxonNode((long) current.get("AphiaID"),TaxonType.valueOf((String) current.get("rank")) ,(String) current.get("scientificname"));
- nodes[n]= curNode;
+ curNode = new TaxonNode((long) current.get("AphiaID"), TaxonType.valueOf((String) current.get("rank")),
+ (String) current.get("scientificname"));
+ nodes[n] = curNode;
n++;
}
- //If child is null, return
- if ((JSONObject) current.get("child") == null )
+ // If child is null, return
+ if ((JSONObject) current.get("child") == null)
return n;
arraysize = parseIdCall(nodes, child, n);
return arraysize;
}
-
+
}