From 492b47a063cbbbaa2702ff9b1cf61c1aba102cab Mon Sep 17 00:00:00 2001
From: Winnie <liang15@mcmaster.ca>
Date: Wed, 7 Mar 2018 15:47:20 -0500
Subject: [PATCH] - Link with BioTree and Records ADT - Improve naming
---
src/biotree/FileProcessor.java | 56 ++++++++++++++++++++++------------
1 file changed, 36 insertions(+), 20 deletions(-)
diff --git a/src/biotree/FileProcessor.java b/src/biotree/FileProcessor.java
index ff33594..5d0fce8 100644
--- a/src/biotree/FileProcessor.java
+++ b/src/biotree/FileProcessor.java
@@ -7,7 +7,6 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
- * @author
* This class reads and parses files in the format of occurences.csv
* It provides methods to get chunks of data.
*
@@ -40,7 +39,7 @@ public class FileProcessor {
* Reads file at path.
* Calls parse() automatically
*/
- private static void read() {
+ private static void initProcessing() {
FileReader fr;
BufferedReader br;
@@ -69,15 +68,15 @@ public class FileProcessor {
/**
* Parses out data from string
- * "scientificName" in raw data heading = species name
*
- * @param currentLine - A line/row of data
+ * @param currentLine, a line/row of data
*/
- private static void parse(String currentLine) {
+ // TODO: Fix spahgetti code where taxonId needs to be converted to a string when it is received from biotree.
+ private static void parse(String currentLine) throws IOException {
String[] splitLine = currentLine.split(",");
- String eventId = null, taxId = null, occurrenceId, latitude, longitude, month= null, year=null, day=null, individualCount;
+ String eventId = null, occurId, taxonId = null, individualCount, latitude, longitude, year=null, month= null, day=null;
- occurrenceId = splitLine[3];
+ occurId = splitLine[3];
individualCount = splitLine[4];
Pattern patternEventId = Pattern.compile("OP_ID (\\d+)");
@@ -107,29 +106,46 @@ public class FileProcessor {
Pattern patternTaxId = Pattern.compile(":(\\d+)");
Matcher matchTaxId = patternTaxId.matcher(splitLine[11]);
if(matchTaxId.find()) {
- taxId = matchTaxId.group(1);
+ taxonId = matchTaxId.group(1);
}
else {
// TODO: Throw Exception?
System.out.println("Could not parse TaxId. String may be unique or missing.");
}
- //Taxonomy Info [12-18] - Using a species ADT instead?
+ // Call BioTree
+ if(taxonId != null) {
+ BioTree.processRecord(Integer.parseInt(taxonId));
+ }
+ else if (splitLine[12] != "NA") {
+ try{
+ taxonId = Integer.toString(BioTree.processRecord(splitLine[12]));
+ } catch(IOException e) {
+ System.out.println("No Taxon ID or Scientific Name");
+ }
+ }
+
+ // Create Record Object
+ createRecord(Integer.parseInt(eventId), occurId, Integer.parseInt(taxonId), Integer.parseInt(individualCount), Float.parseFloat(latitude), Float.parseFloat(longitude), Integer.parseInt(year), Integer.parseInt(month), Integer.parseInt(day));
+
- // At this point, adt constructor will be called to create the object.
// Testing ONLY Print lines
- System.out.println("Occurence Id:" + occurrenceId);
- System.out.println("Ind. Count:" + individualCount);
- System.out.println("event Id:" + eventId);
- System.out.println("Year:" + year);
- System.out.println("Month:" + month);
- System.out.println("Day:" + day);
- System.out.println("lat:" + latitude);
- System.out.println("long:" + longitude);
- System.out.println("tax Id:" + taxId);
+// System.out.println("Occurence Id:" + occurId);
+// System.out.println("Ind. Count:" + individualCount);
+// System.out.println("event Id:" + eventId);
+// System.out.println("Year:" + year);
+// System.out.println("Month:" + month);
+// System.out.println("Day:" + day);
+// System.out.println("lat:" + latitude);
+// System.out.println("long:" + longitude);
+// System.out.println("tax Id:" + taxonId);
+ }
+
+ public static Record createRecord(int eventId, String occurId, int taxonId, int individualCount, float latitude, float longitude, int year, int month, int day) {
+ return new Record(eventId, occurId, taxonId, individualCount, latitude, longitude, year, month, day);
}
public static void main(String[] args) {
- read();
+ initProcessing();
}
}
--
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