| @@ -10,27 +10,16 @@ |
| import com.mongodb.client.FindIterable; |
| import com.mongodb.client.MongoCollection; |
| import com.mongodb.client.MongoDatabase; |
| -import com.mongodb.client.model.UpdateOptions; |
| +import csip.annotations.*; |
| import javax.ws.rs.Path; |
| -import oms3.annotations.*; |
| import csip.ModelDataService; |
| import csip.SessionLogger; |
| -import java.io.File; |
| -import java.io.FileNotFoundException; |
| -import java.io.IOException; |
| -import java.text.ParseException; |
| -import java.text.SimpleDateFormat; |
| import java.util.ArrayList; |
| -import java.util.Arrays; |
| -import java.util.Collections; |
| -import java.util.Iterator; |
| import java.util.List; |
| -import java.util.TimeZone; |
| import org.bson.Document; |
| import org.codehaus.jettison.json.JSONArray; |
| import org.codehaus.jettison.json.JSONException; |
| import org.codehaus.jettison.json.JSONObject; |
| -import utils.TimeseriesTable; |
| |
| /** |
| * Mongodb timeseries data deletion |
| @@ -39,6 +28,8 @@ |
| */ |
| @Name("Timeseries delete") |
| @Description("Delete a timeseries collection or document in mongo.") |
| +@Author(org = "CSU") |
| +@License(License.MIT) |
| @Path("m/delete/1.0") |
| public class V1_0 extends ModelDataService { |
| |
| @@ -46,6 +37,7 @@ |
| MongoDatabase db; |
| JSONObject results = new JSONObject(); |
| |
| + |
| protected void open(String mongoclienturi) { |
| MongoClientURI u = new MongoClientURI(mongoclienturi); |
| mongo = new MongoClient(u); |
| @@ -69,25 +61,29 @@ |
| String mongo_uri = getStringParam("mongo_uri"); |
| String mongo_collection = getStringParam("mongo_collection"); |
| JSONArray ids = getJSONArrayParam("ids", null); |
| + |
| if (ids != null) { |
| - deleteIds(mongo_uri, mongo_collection, ids, LOG); |
| + deleteIds(mongo_uri, mongo_collection, ids); |
| } else { |
| // If no ids specified, then delete the collection. |
| - deleteCollection(mongo_uri, mongo_collection, LOG); |
| + deleteCollection(mongo_uri, mongo_collection); |
| } |
| } |
| - |
| - public void deleteCollection(String mongo_uri, String mongo_collection, SessionLogger LOG) throws JSONException { |
| + |
| + |
| + public void deleteCollection(String mongo_uri, String mongo_collection) throws JSONException { |
| open(mongo_uri); |
| MongoCollection<Document> collection = db.getCollection(mongo_collection); |
| collection.drop(); |
| results.put("deleted_collection", mongo_collection); |
| + close(); |
| } |
| |
| - public void deleteIds(String mongo_uri, String mongo_collection, JSONArray ids, SessionLogger LOG) throws JSONException { |
| + |
| + public void deleteIds(String mongo_uri, String mongo_collection, JSONArray ids) throws JSONException { |
| open(mongo_uri); |
| MongoCollection<Document> collection = db.getCollection(mongo_collection); |
| - |
| + |
| List<String> ids_list = new ArrayList(); |
| for (int i = 0; i < ids.length(); i++) { |
| ids_list.add(ids.getString(i)); |
| @@ -95,16 +91,16 @@ |
| |
| List<String> deleted_ids = new ArrayList(); |
| FindIterable<Document> c = collection.find(); |
| - for (Document finddoc: c) { |
| - String find_id = (String)finddoc.get("_id"); |
| + for (Document finddoc : c) { |
| + String find_id = (String) finddoc.get("_id"); |
| if (ids_list.contains(find_id)) { |
| LOG.info("Deleting existing doc"); |
| collection.deleteOne(finddoc); |
| deleted_ids.add(find_id); |
| } |
| } |
| - |
| results.put("deleted_document_ids", new JSONArray(deleted_ids)); |
| + close(); |
| } |
| |
| |
| @@ -112,16 +108,17 @@ |
| protected void postProcess() throws Exception { |
| putResult("result", results); |
| } |
| - |
| - public static void main(String [] args) throws JSONException { |
| + |
| + |
| + public static void main(String[] args) throws JSONException { |
| V1_0 timeseries = new V1_0(); |
| - SessionLogger LOG = new SessionLogger(); |
| JSONArray delete_ids = new JSONArray(); |
| delete_ids.put("test_ref"); |
| - timeseries.deleteIds("mongodb://eds0.engr.colostate.edu:27017/csip_timeseries", "test_coll", delete_ids, LOG); |
| - timeseries.deleteCollection("mongodb://eds0.engr.colostate.edu:27017/csip_timeseries", "test_coll", LOG); |
| + timeseries.deleteIds("mongodb://eds0.engr.colostate.edu:27017/csip_timeseries", "test_coll", delete_ids); |
| + timeseries.deleteCollection("mongodb://eds0.engr.colostate.edu:27017/csip_timeseries", "test_coll"); |
| } |
| - |
| + |
| + |
| public static String[] toStringArray(List<String> data) { |
| return (String[]) data.stream().map(String::toString).toArray(); |
| } |
| @@ -12,7 +12,6 @@ |
| import com.mongodb.client.MongoDatabase; |
| import com.mongodb.client.model.UpdateOptions; |
| import javax.ws.rs.Path; |
| -import oms3.annotations.*; |
| import csip.ModelDataService; |
| import csip.SessionLogger; |
| import java.io.File; |
| @@ -29,7 +28,8 @@ |
| import org.codehaus.jettison.json.JSONException; |
| import org.codehaus.jettison.json.JSONObject; |
| import utils.TimeseriesTable; |
| - |
| +import csip.annotations.*; |
| + |
| /** |
| * Mongodb timeseries data insertion |
| * |
| @@ -37,6 +37,9 @@ |
| */ |
| @Name("Timeseries insert") |
| @Description("Update a timeseries collection in mongo.") |
| +@Author(org="CSU") |
| +@License(License.MIT) |
| + |
| @Path("m/insert/1.0") |
| public class V1_0 extends ModelDataService { |
| |
| @@ -53,7 +56,6 @@ |
| if (!u.getDatabase().equals("csip_timeseries")) { |
| throw new RuntimeException("Can only modify csip_timeseries collection"); |
| } |
| - |
| db = mongo.getDatabase(u.getDatabase()); |
| } |
| |
| @@ -75,11 +77,13 @@ |
| String date_fmt = getStringParam("date_format"); |
| JSONArray locationArray = getJSONArrayParam("location"); |
| List<Double> location = Arrays.asList(Double.parseDouble(locationArray.get(0).toString()), Double.parseDouble(locationArray.get(1).toString())); |
| + |
| run(mongo_uri, mongo_collection, doc_id, data_file, data_col, metadata, date_fmt, location, LOG); |
| } |
| |
| - public void run(String mongo_uri, String mongo_collection, String doc_id, File data_file, String data_col, JSONObject metadata, |
| + void run(String mongo_uri, String mongo_collection, String doc_id, File data_file, String data_col, JSONObject metadata, |
| String date_fmt, List<Double> location, SessionLogger LOG) throws FileNotFoundException, IOException, JSONException, ParseException { |
| + |
| open(mongo_uri); |
| MongoCollection<Document> collection = db.getCollection(mongo_collection); |
| |
| @@ -127,6 +131,7 @@ |
| } |
| results = new JSONObject(); |
| results.put("updated_document_id", doc.get("_id").toString()); |
| + close(); |
| } |
| |
| |
| @@ -14,10 +14,10 @@ |
| import com.mongodb.client.model.Aggregates; |
| import com.mongodb.client.model.Filters; |
| import javax.ws.rs.Path; |
| -import oms3.annotations.*; |
| import csip.ModelDataService; |
| import csip.ServiceException; |
| import csip.SessionLogger; |
| +import csip.annotations.*; |
| import java.io.FileNotFoundException; |
| import java.io.IOException; |
| import java.text.ParseException; |
| @@ -39,6 +39,7 @@ |
| import org.codehaus.jettison.json.JSONObject; |
| import java.util.logging.Level; |
| import java.util.logging.Logger; |
| +import org.apache.catalina.ant.ServerinfoTask; |
| |
| /** |
| * Mongodb timeseries data insertion |
| @@ -47,6 +48,8 @@ |
| */ |
| @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 { |
| |
| @@ -55,6 +58,7 @@ |
| |
| JSONArray results = new JSONArray(); |
| |
| + |
| protected void open(String mongoclienturi) { |
| MongoClientURI u = new MongoClientURI(mongoclienturi); |
| mongo = new MongoClient(u); |
| @@ -79,17 +83,21 @@ |
| boolean metadata_only = getBooleanParam("metadata_only", true); |
| boolean compute_stats = getBooleanParam("compute_stats", false); |
| 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, compute_stats, LOG); |
| + JSONObject search_feature = getJSONParam("search_feature", null); |
| + |
| + run(mongo_uri, mongo_collection, search_feature, search_id, start_date, end_date, metadata_only, compute_stats); |
| } |
| - |
| - 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, boolean compute_stats, SessionLogger LOG) throws JSONException, ServiceException { |
| + |
| + |
| + @Override |
| + protected void postProcess() throws Exception { |
| + putResult("result", results); |
| + } |
| + |
| + |
| + 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, boolean compute_stats) throws JSONException, ServiceException { |
| + |
| open(mongo_uri); |
| MongoCollection<Document> collection = db.getCollection(mongo_collection); |
| |
| @@ -118,37 +126,39 @@ |
| c = collection.find(Filters.eq("_id", search_id)); |
| } |
| } |
| - for (Document doc: c) { |
| + for (Document doc : c) { |
| JSONObject res = getResult(collection, doc, start_date, end_date, metadata_only, compute_stats); |
| 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); |
| + throw new ServiceException(ex); |
| } |
| AggregateIterable<Document> c = collection.aggregate(agg_match); |
| - for (Document doc: c) { |
| + for (Document doc : c) { |
| JSONObject res = getResult(collection, doc, start_date, end_date, metadata_only, compute_stats); |
| results.put(res); |
| } |
| } |
| } |
| + close(); |
| } |
| |
| + |
| private JSONObject getResult(MongoCollection<Document> c, Document doc, Date start_date, Date end_date, |
| boolean metadata_only, boolean compute_stats) throws JSONException { |
| - String date_fmt = (String)doc.get("date_fmt"); |
| + 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<String> header = (ArrayList) doc.get("header"); |
| + List<List<Object>> data = (ArrayList) doc.get("data"); |
| JSONArray output = new JSONArray(); |
| List<List<Object>> filtered = new ArrayList(); |
| JSONObject statResult = new JSONObject(); |
| @@ -195,7 +205,6 @@ |
| } |
| } |
| |
| - |
| if (compute_stats) { |
| Document statsDoc = new Document("_id", null); |
| List<String> stats = Arrays.asList("min", "max", "avg", "stdDevPop"); |
| @@ -223,39 +232,33 @@ |
| } |
| } |
| } |
| - |
| + |
| JSONObject res = new JSONObject(); |
| res.put("_id", doc.get("_id")); |
| - Document location = (Document)doc.get("location"); |
| - List<Double> coords = (List<Double>)location.get("coordinates"); |
| + 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"); |
| + Document metadata = (Document) doc.get("metadata"); |
| res.put("metadata", new JSONObject(metadata.toJson())); |
| |
| if (compute_stats) { |
| res.put("statistics", statResult); |
| } |
| |
| - |
| 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(); |
| + 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)) |
| - ) |
| + new Document("$geoWithin", |
| + new Document("$geometry", Document.parse(geom)) |
| + ) |
| ); |
| if (search_id != null) { |
| // Check for object ID (will be a hexidecimal string) |
| @@ -272,52 +275,52 @@ |
| agg_match.add(new_match); |
| return agg_match; |
| } |
| - |
| - public static void main(String [] args) throws FileNotFoundException, IOException, JSONException, ParseException, ServiceException { |
| + |
| + |
| + public static void main(String[] args) throws FileNotFoundException, IOException, JSONException, ParseException, ServiceException { |
| 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(); |
| + 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" |
| + + " }"); |
| 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, true, LOG); |
| + timeseries.run("mongodb://eds0.engr.colostate.edu:27017/csip_timeseries", "test_coll", searchFeature, search_id, "2014-04-04", "2014-05-08", false, true); |
| } |
| } |