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Some query changes

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Changes in server code required update of some of the json for existing
queries.
This commit is contained in:
Douglas Gillespie 2023-05-07 20:06:59 +01:00
parent 00410d2017
commit 49843b405f
4 changed files with 82 additions and 10 deletions
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14
src/tethys/TethysControl.java
View File

@ -32,6 +32,7 @@ import tethys.dbxml.DBXMLConnect;
import tethys.dbxml.DBXMLQueries;
import tethys.dbxml.ServerStatus;
import tethys.dbxml.TethysException;
import tethys.dbxml.TethysQueryException;
import tethys.deployment.DeploymentHandler;
import tethys.detection.DetectionsHandler;
import tethys.niluswraps.PDeployment;
@ -515,17 +516,24 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
String msg = "";
if (stack != null) {
msg = "Caused in";
for (int i = 0; i < Math.min(stack.length, 2); i++) {
for (int i = 0; i < Math.min(stack.length, 3); i++) {
msg += "<br>" + stack[i].getClassName() + "." + stack[i].getMethodName();
}
}
if (tethysException instanceof TethysQueryException) {
TethysQueryException tqe = (TethysQueryException) tethysException;
// msg += tqe.
}
String xml = tethysException.getXmlError();
if (xml != null) {
// msg += "<textarea rows=\"6\" cols=\"80\" style=\"border:none;\">" + xml + "</textarea>";
/**
* html can't handle the < and > in xml without getting very confused
* but it seems to work fine if they are replaced with their html codes.
*/
xml = xml.replace("<", "&lt;");
xml = xml.replace(">", "&gt;");
xml = xml.replace("\n", "<br>");
// msg += xml;
msg += "<pre>"+xml+"</pre>";
}
WarnOnce.showWarning(title, msg, WarnOnce.WARNING_MESSAGE);

73
src/tethys/dbxml/DBXMLQueries.java
View File

@ -30,6 +30,8 @@ import nilus.Helper;
import tethys.TethysControl;
import tethys.TethysTimeFuncs;
import tethys.output.TethysExportParams;
import warnings.PamWarning;
import warnings.WarningSystem;
/**
* Some standard queries we're going to want to make from various
@ -41,11 +43,14 @@ public class DBXMLQueries {
private TethysControl tethysControl;
private DBXMLConnect dbXMLConnect;
private PamWarning queryWarning;
public DBXMLQueries(TethysControl tethysControl, DBXMLConnect dbXMLConnect) {
super();
this.tethysControl = tethysControl;
this.dbXMLConnect = dbXMLConnect;
queryWarning = new PamWarning("Tethys Query", null, 0);
}
/**
@ -57,7 +62,63 @@ public class DBXMLQueries {
* @throws TethysQueryException
*/
private DBQueryResult executeQuery(String jsonQueryString) throws TethysQueryException {
long t1 = System.currentTimeMillis();
DBQueryResult result = null;
TethysQueryException tException = null;
try {
result = executeQueryT(jsonQueryString);
}
catch (TethysQueryException e) {
tException = e;
}
if (result == null) {
// try pinging the server and throw an exception if it's not alive.
ServerStatus serverStatus = tethysControl.getDbxmlConnect().pingServer();
if (serverStatus.ok) {
queryWarning.setWarnignLevel(2);
queryWarning.setWarningMessage("null return from Tethys json query");
queryWarning.setWarningTip(jsonQueryString);
queryWarning.setEndOfLife(Long.MAX_VALUE);
WarningSystem.getWarningSystem().addWarning(queryWarning);
}
else {
queryWarning.setWarnignLevel(2);
if (serverStatus.error != null) {
queryWarning.setWarningMessage(serverStatus.error.getMessage());
}
else {
queryWarning.setWarningMessage("Unknown Tethys server error");
}
queryWarning.setWarningTip(jsonQueryString);
queryWarning.setEndOfLife(Long.MAX_VALUE);
WarningSystem.getWarningSystem().addWarning(queryWarning);
return null;
}
}
long t2 = System.currentTimeMillis();
if (tException != null) {
// display query warning then throw the exception anyway
queryWarning.setWarnignLevel(2);
queryWarning.setWarningMessage("Error running Tethys json query");
queryWarning.setWarningTip(jsonQueryString);
queryWarning.setEndOfLife(Long.MAX_VALUE);
WarningSystem.getWarningSystem().addWarning(queryWarning);
throw tException;
}
else {
// clear warning, but say how long query took still
queryWarning.setWarnignLevel(0);
queryWarning.setWarningMessage(String.format("Tethys json query executed in %4.2f seconds", (double) (t2-t1)/1000.));
queryWarning.setWarningTip(jsonQueryString);
WarningSystem.getWarningSystem().addWarning(queryWarning);
queryWarning.setEndOfLife(t2+10000);
return result;
}
}
private DBQueryResult executeQueryT(String jsonQueryString) throws TethysQueryException {
long t1 = System.currentTimeMillis();
DBXMLConnect dbxmlConnect = tethysControl.getDbxmlConnect();
@ -72,8 +133,6 @@ public class DBXMLQueries {
try {
JerseyClient jerseyClient = dbxmlConnect.getJerseyClient();
// String url = jerseyClient.getURL();
// Queries queries = new Queries(jerseyClient);
queryResult = jerseyClient.queryJSON(jsonQueryString, 0);
@ -81,7 +140,6 @@ public class DBXMLQueries {
}
catch (Exception e) {
// return new DBQueryResult(System.currentTimeMillis()-t1, e);
throw new TethysQueryException("Error running JSON query", jsonQueryString);
}
@ -255,9 +313,10 @@ public class DBXMLQueries {
public ArrayList<String> getDetectionsDocuments(PamDataBlock dataBlock, String deploymentId) {
/**
* first query for Detections documents associated with this deployment and datablock.
* updated May 23
*/
String queryNoDepl = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String queryWithDepl = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"TheDeploymentId\"],\"optype\":\"binary\"}],\"enclose\":1}";
String queryNoDepl = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String queryWithDepl = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Detections/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/DataSource/DeploymentId\",\"TheDeploymentId\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Detections/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String query;
if (deploymentId == null) {
query = queryNoDepl;
@ -589,7 +648,9 @@ public class DBXMLQueries {
* @return
*/
public Detections getDetectionsDocInfo(String detectionsDocName) {
String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\",\"Detections/Description\",\"Detections/DataSource\",\"Detections/Algorithm\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"DetectionsDocName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String oldqueryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\",\"Detections/Description\",\"Detections/DataSource\",\"Detections/Algorithm\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"DetectionsDocName\"],\"optype\":\"binary\"}],\"enclose\":1}";
// updated May 23
String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Detections/Id\",\"Detections/Description\",\"Detections/DataSource\",\"Detections/Algorithm\",\"Detections/QualityAssurance\",\"Detections/UserId\",\"Detections/MetadataInfo\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"DetectionsDocName\"],\"optype\":\"binary\"}],\"enclose\":1}";
String query = queryBase.replace("DetectionsDocName", detectionsDocName);
DBQueryResult queryResult;
try {

3
src/tethys/dbxml/TethysQueryException.java
View File

@ -2,6 +2,9 @@ package tethys.dbxml;
public class TethysQueryException extends TethysException {
private static final long serialVersionUID = 1L;
private String queryString;
public TethysQueryException(String message, String queryString) {

2
src/warnings/WarningSystem.java
View File

@ -149,7 +149,7 @@ public class WarningSystem {
* Remove old warnings.
*/
private synchronized void removeOldWarnings() {
long now = PamCalendar.getTimeInMillis();
long now = System.currentTimeMillis();
ListIterator<PamWarning> it = warnings.listIterator();
int removals = 0;
while (it.hasNext()) {