V1_0.java [src/java/m/timeseries/query] Revision: 0a3f7328a951601d2eb54e34681b7c326dd9cdad Date: Thu Aug 30 16:54:08 MDT 2018
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package m.timeseries.query;
import com.mongodb.MongoClient;
import com.mongodb.MongoClientURI;
import com.mongodb.client.AggregateIterable;
import com.mongodb.client.FindIterable;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
import com.mongodb.client.model.Filters;
import javax.ws.rs.Path;
import csip.ModelDataService;
import csip.ServiceException;
import csip.SessionLogger;
import csip.annotations.*;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.time.LocalDate;
import java.time.ZoneId;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.TimeZone;
import org.bson.Document;
import org.bson.types.ObjectId;
import org.bson.conversions.Bson;
import org.codehaus.jettison.json.JSONArray;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import java.util.logging.Level;
import java.util.logging.Logger;
/**
* Mongodb timeseries data insertion
*
* @author Dave Patterson
*/
@Name("Timeseries query")
@Description("Query a timeseries collection in mongo.")
@Author(org = "CSU")
@License(License.MIT)
@Path("m/query/1.0")
public class V1_0 extends ModelDataService {
MongoClient mongo;
MongoDatabase db;
JSONArray results = new JSONArray();
protected void open(String mongoclienturi) {
MongoClientURI u = new MongoClientURI(mongoclienturi);
mongo = new MongoClient(u);
if (u.getDatabase() == null) {
throw new RuntimeException("Missing database in mongo uri: " + mongoclienturi);
}
db = mongo.getDatabase(u.getDatabase());
}
protected void close() {
mongo.close();
}
@Override
public void doProcess() throws Exception {
String mongo_uri = getStringParam("mongo_uri");
String mongo_collection = getStringParam("mongo_collection");
String start_date = getStringParam("start_date", null);
String end_date = getStringParam("end_date", null);
boolean metadata_only = getBooleanParam("metadata_only", true);
String search_id = getStringParam("search_id", null);
JSONObject search_feature;
try {
search_feature = getJSONParam("search_feature", null);
} catch (ServiceException ex) {
throw new RuntimeException(ex);
}
run(mongo_uri, mongo_collection, search_feature, search_id, start_date, end_date, metadata_only, LOG);
}
public void run(String mongo_uri, String mongo_collection, JSONObject search_feature, String search_id,
String start_date_str, String end_date_str, boolean metadata_only, SessionLogger LOG) throws JSONException {
open(mongo_uri);
MongoCollection<Document> collection = db.getCollection(mongo_collection);
LocalDate start_date = null;
LocalDate end_date = null;
if (start_date_str != null) {
start_date = LocalDate.parse(start_date_str);
end_date = LocalDate.parse(end_date_str);
}
if (search_feature == null) {
FindIterable<Document> c;
if (search_id == null) {
c = collection.find();
} else {
// Check for object ID (will be a hexidecimal string)
boolean id_test = search_id.matches("\\p{XDigit}+");
if (id_test) {
ObjectId search_objid = new ObjectId(search_id);
c = collection.find(Filters.eq("_id", search_objid));
} else {
c = collection.find(Filters.eq("_id", search_id));
}
}
for (Document doc : c) {
JSONObject res = getResult(doc, start_date, end_date, metadata_only);
results.put(res);
}
} else {
JSONArray features = search_feature.getJSONArray("features");
for (int i = 0; i < features.length(); i++) {
JSONObject feat = features.getJSONObject(i);
List<Bson> agg_match = null;
try {
agg_match = getMatch(feat, search_id);
} catch (IOException ex) {
Logger.getLogger(V1_0.class.getName()).log(Level.SEVERE, null, ex);
}
AggregateIterable<Document> c = collection.aggregate(agg_match);
for (Document doc : c) {
JSONObject res = getResult(doc, start_date, end_date, metadata_only);
results.put(res);
}
}
}
}
private JSONObject getResult(Document doc, LocalDate start_date, LocalDate end_date, boolean metadata_only) throws JSONException {
String date_fmt = (String) doc.get("date_fmt");
SimpleDateFormat ft = new SimpleDateFormat(date_fmt);
ft.setTimeZone(TimeZone.getTimeZone("UTC"));
List<String> header = (ArrayList) doc.get("header");
List<List<Object>> data = (ArrayList) doc.get("data");
JSONArray output = new JSONArray();
List<List<Object>> filtered = new ArrayList();
if (!metadata_only) {
// Filter by period and format date
for (int irow = 0; irow < data.size(); irow++) {
Date dt = (Date) data.get(irow).get(0);
LocalDate dt_local = dt.toInstant().atZone(ZoneId.of("UTC")).toLocalDate();
if (start_date != null && dt_local.isBefore(start_date)) {
continue;
} else if (end_date != null && dt_local.isAfter(end_date)) {
break;
}
data.get(irow).set(0, ft.format(dt));
filtered.add(data.get(irow));
}
}
JSONObject res = new JSONObject();
res.put("_id", doc.get("_id"));
Document location = (Document) doc.get("location");
List<Double> coords = (List<Double>) location.get("coordinates");
res.put("location", coords);
res.put("header", header);
if (!metadata_only) {
res.put("data", filtered);
}
Document metadata = (Document) doc.get("metadata");
res.put("metadata", new JSONObject(metadata.toJson()));
return res;
}
@Override
protected void postProcess() throws Exception {
putResult("result", results);
}
public List<Bson> getMatch(JSONObject feat, String search_id) throws JSONException, IOException {
String geom = feat.getJSONObject("geometry").toString();
Document match_arg = new Document("location",
new Document("$geoWithin",
new Document("$geometry", Document.parse(geom))
)
);
if (search_id != null) {
// Check for object ID (will be a hexidecimal string)
boolean id_test = search_id.matches("\\p{XDigit}+");
if (id_test) {
ObjectId search_objid = new ObjectId(search_id);
match_arg.put("_id", search_objid);
} else {
match_arg.put("_id", search_id);
}
}
Document new_match = new Document("$match", match_arg);
List<Bson> agg_match = new ArrayList<>();
agg_match.add(new_match);
return agg_match;
}
public static void main(String[] args) throws FileNotFoundException, IOException, JSONException, ParseException {
V1_0 timeseries = new V1_0();
JSONObject searchFeature = new JSONObject("{\n"
+ " \"type\": \"FeatureCollection\",\n"
+ " \"features\": [\n"
+ " {\n"
+ " \"geometry\": {\n"
+ " \"type\": \"MultiPolygon\",\n"
+ " \"coordinates\": [\n"
+ " [\n"
+ " [\n"
+ " [\n"
+ " -105.09928580027,\n"
+ " 40.701406829918\n"
+ " ],\n"
+ " [\n"
+ " -105.09447928172,\n"
+ " 40.365324016903\n"
+ " ],\n"
+ " [\n"
+ " -104.72849722611,\n"
+ " 40.358522384503\n"
+ " ],\n"
+ " [\n"
+ " -104.72437735306,\n"
+ " 40.701927386425\n"
+ " ],\n"
+ " [\n"
+ " -105.09928580027,\n"
+ " 40.701406829918\n"
+ " ]\n"
+ " ]\n"
+ " ]\n"
+ " ]\n"
+ " },\n"
+ " \"type\": \"Feature\",\n"
+ " \"properties\": {\n"
+ " \"gid\": 1,\n"
+ " \"name\": \"gid 1\"\n"
+ " }\n"
+ " }\n"
+ " ]\n"
+ " }");
SessionLogger LOG = new SessionLogger();
String search_id = null;
timeseries.run("mongodb://eds0.engr.colostate.edu:27017/csip_timeseries", "test_coll", searchFeature, search_id, "2014-04-04", "2014-05-08", false, LOG);
}
}