Merge pull request #1806 from Caltech-IPAC/FIREFLY-1793-rubin-fixes

Firefly-1793: Fixes some rubin issues

Author: robyww

docs/release-notes.md

@@ -8,7 +8,8 @@
 
 
 ## Version 2025.3
-- 2025.3.4 - (June 26, 2025), _docker tag_: `2025.3.4`, `2025.3`, `latest`
+- 2025.3.5 - (July 1, 2025), _docker tag_: `2025.3.5`, `2025.3`, `latest`
+- 2025.3.4 - (June 26, 2025), _docker tag_: `2025.3.4`
 - 2025.3.3 - (June 20, 2025), _docker tag_: `2025.3.3`
 - 2025.3.2 - (June 16, 2025), _docker tag_: `2025.3.2`
 - 2025.3.1 - (June 9, 2025), _docker tag_: `2025.3.1`
@@ -73,13 +74,15 @@
 
 
 ### _Patches 2025.3_
+- 2025.3.5
+  - Fixed: Images: mouse readout with some compressed images- Firefly-1793,Firefly-1792,Firefly-1789  ([PR](https://github.com/Caltech-IPAC/firefly/pull/1804))
 - 2025.3.4 
   - Timeseries: improve save table filename- Firefly-1354 ([PR](https://github.com/Caltech-IPAC/firefly/pull/1802))
   - Better messaging for Position Cols in TAP Spatial Search- Firefly-1677 ([PR](https://github.com/Caltech-IPAC/firefly/pull/1803))
-  - Fixed: TAP and SIA issues- Firefly-1786 ([PR](https://github.com/Caltech-IPAC/firefly/pull/1804))
+  - Fixed: TAP and SIA issues- Firefly-1786, rubin DM-51532  ([PR](https://github.com/Caltech-IPAC/firefly/pull/1804))
   - Fixed: Image expansion in bi-view mode fails ([commit](https://github.com/Caltech-IPAC/firefly/commit/1d2c3f222cb6d8611f0361ffa4ad5aaa63d278f5))
 - 2025.3.3 
-  - Sanitize header values when logging and handle HiPS /properties url-  Patch ([PR](https://github.com/Caltech-IPAC/firefly/pull/1801))
+  - Sanitize header values when logging and handle HiPS /properties url- (rubin DM-51480) Patch ([PR](https://github.com/Caltech-IPAC/firefly/pull/1801))
   - Improve Redis configuration and administration features- FIREFLY-1779 ([PR](https://github.com/Caltech-IPAC/firefly/pull/1794))
 - 2025.3.2 
   - Fixed: TAP: Upload fails when using a `*` in the ADQL statement-  Firefly-1581 ([PR](https://github.com/Caltech-IPAC/firefly/pull/1796))

src/firefly/java/edu/caltech/ipac/firefly/core/background/JobManager.java

@@ -65,7 +65,7 @@ public class JobManager {
     public static final String BG_INFO = "background.info";
     public static final String ALL_JOB_CACHE_KEY = "ALL_JOB_INFOS"; // cache key for all job infos
     public static final long CLEANUP_INTVL_MINS = AppProperties.getIntProperty("job.cleanup.interval", 60);     // run cleanup once every 60 minutes
-    private static final int KEEP_ALIVE_INTERVAL = AppProperties.getIntProperty("job.keepalive.interval", 30);  // default keepalive interval in seconds
+    private static final int KEEP_ALIVE_INTERVAL = AppProperties.getIntProperty("job.keepalive.interval", 60);  // default keepalive interval in seconds
     private static final int WAIT_COMPLETE = AppProperties.getIntProperty("job.wait.complete", 1);              // wait for complete after submit in seconds
     private static final int MAX_PACKAGERS = AppProperties.getIntProperty("job.max.packagers", 10);             // maximum number of simultaneous packaging threads
     private static final int JOB_EXPIRY_HOURS = AppProperties.getIntProperty("job.expiry.hours", 24*14);        // Time in hours to keep a job after it has ended.  Default to 14 days.

src/firefly/java/edu/caltech/ipac/firefly/server/RequestOwner.java

@@ -3,7 +3,6 @@
  */
 package edu.caltech.ipac.firefly.server;
 
-import edu.caltech.ipac.firefly.core.Util;
 import edu.caltech.ipac.firefly.data.userdata.UserInfo;
 import edu.caltech.ipac.firefly.server.events.FluxAction;
 import edu.caltech.ipac.firefly.server.events.ServerEventManager;
@@ -266,6 +265,7 @@ private void notifyClient(UserInfo userInfo) {
             action.setValue(getSsoAdapter().getLoginUrl(""), "login_url");
             action.setValue(getSsoAdapter().getLogoutUrl(""), "logout_url");
         }
+        LOG.info("notifyClient new User info: " + userInfo);
         ServerEventManager.fireAction(action);
     }
 

src/firefly/java/edu/caltech/ipac/firefly/server/servlets/CommandService.java

@@ -4,8 +4,9 @@
 package edu.caltech.ipac.firefly.server.servlets;
 
 import edu.caltech.ipac.firefly.server.ServerCommandAccess;
-import edu.caltech.ipac.firefly.server.util.Logger;
+import edu.caltech.ipac.firefly.server.ServerContext;
 import edu.caltech.ipac.firefly.server.SrvParam;
+import edu.caltech.ipac.firefly.server.util.Logger;
 import org.json.simple.JSONObject;
 
 import javax.servlet.http.HttpServletRequest;
@@ -67,7 +68,13 @@ protected void processRequest(HttpServletRequest req, HttpServletResponse res) t
             String cmd = sp.getCommandKey();
             ServerCommandAccess.HttpCommand command = ServerCommandAccess.getCommand(cmd);
             command.processRequest(req, res, sp);
-            Logger.briefDebug(String.format("CommandService: %s : %dms", cmd, System.currentTimeMillis() - start));
+            var sso= ServerContext.getRequestOwner().getSsoAdapter();
+            String userInfoStr= "";
+            if (sso!=null) {
+                var ui= sso.getUserInfo();
+                if (ui!=null) userInfoStr= ui.toString();
+            }
+            Logger.briefInfo(String.format("CommandService: %s (%s): %dms", cmd, userInfoStr, System.currentTimeMillis() - start));
         } catch (Exception ex) {
             LOGGER.error(ex);
             HashMap<String, String> errors = new HashMap<>();

src/firefly/java/edu/caltech/ipac/visualize/plot/plotdata/FitsReadFactory.java

@@ -18,6 +18,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Arrays;
 
 /**
  * @author Trey Roby
@@ -38,8 +39,10 @@ public static FitsRead[] createFitsReadArray(Fits fits) throws FitsException {
 
     public static FitsRead[] createFitsReadArray(BasicHDU<?>[] HDUs, File f, boolean clearHdu) throws FitsException {
         if (HDUs == null) throw new FitsException(BAD_FORMAT_MSG);
+        var headersSizesList= Arrays.stream(HDUs).map(hdu -> hdu.getHeader().getSize()).toList();
+        var headersOffsetsList= Arrays.stream(HDUs).map(hdu -> hdu.getHeader().getFileOffset()).toList();
 
-        BasicHDU<?> [] imageHDUs= FitsReadUtil.getImageHDUArray(HDUs, true);
+        BasicHDU<?> [] imageHDUs= FitsReadUtil.getImageHDUArray(HDUs, true, headersSizesList, headersOffsetsList);
         BasicHDU<?> hdu;
         Header zeroHeader= getZeroHeader(HDUs) ;
         confirmHasImageData(imageHDUs,HDUs);

src/firefly/java/edu/caltech/ipac/visualize/plot/plotdata/FitsReadUtil.java

@@ -103,10 +103,11 @@ public static UncompressFitsInfo createdUncompressVersionOfFile(BasicHDU<?>[] HD
         fits.write(retFile);
         closeFits(fits);
         Fits retReadFits= new Fits(retFile);
-        return new UncompressFitsInfo(retFile,fits.read(), retReadFits);
+        BasicHDU<?>[] inHDUs= retReadFits.read();
+        return new UncompressFitsInfo(retFile,inHDUs, retReadFits);
     }
 
-    public static BasicHDU<?>[] getImageHDUArray(BasicHDU<?>[] HDUs, boolean onlyFireCubeHdu) {
+    public static BasicHDU<?>[] getImageHDUArray(BasicHDU<?>[] HDUs, boolean onlyFireCubeHdu, List<Long> headersSizesList, List<Long> headersOffsetsList) {
         ArrayList<BasicHDU<?>> HDUList = new ArrayList<>();
 
         String delayedExceptionMsg = null; // the exception can be ignored if HDUList size is greater than 0
@@ -144,7 +145,7 @@ else if (naxis == 1) {
 
 
             if (goodImage) {
-                insertPositionIntoHeader(header, j, hdu.getFileOffset());
+                insertPositionIntoHeader(header, j, headersSizesList.get(j), headersOffsetsList.get(j));
 
                 int naxis3 = header.getIntValue("NAXIS3", -1);
                 if ((naxis > 2) && (naxis3 > 1)) { //it is a cube data
@@ -167,10 +168,9 @@ else if (naxis == 1) {
 
 
 
-    private static void insertPositionIntoHeader(Header header, int pos, long hduOffset) {
+    private static void insertPositionIntoHeader(Header header, int pos, long headerSize, long hduOffset) {
         if (hduOffset < 0) hduOffset = 0;
         if (pos < 0) pos = 0;
-        long headerSize = getHeaderSize(header);
         int bitpix = header.getIntValue("BITPIX", -1);
         header.addLine(new HeaderCard(SPOT_HS, headerSize, "Header block size on disk (added by Firefly)"));
         header.addLine(new HeaderCard(SPOT_EXT, pos, "Extension Number (added by Firefly)"));
@@ -350,7 +350,7 @@ private static float[] reversePixData(int naxis1, int naxis2, float[] float1d) {
     }
 
     public static long getHeaderSize(Header header) {
-        return header.getOriginalSize() > 0 ? header.getOriginalSize() : header.getSize();
+           return header.getOriginalSize() > 0 ? header.getOriginalSize() : header.getSize();
     }
 
 

src/firefly/js/ui/FireflyRoot.jsx

@@ -1,5 +1,6 @@
 import React, {useEffect} from 'react';
 import {ScopedCssBaseline, extendTheme, CssVarsProvider, useColorScheme, GlobalStyles} from '@mui/joy';
+import {getBoolean, isDefined, toBoolean} from '../util/WebUtil';
 import {AppPropertiesCtx} from './AppPropertiesCtx.jsx';
 
 import {defaultTheme} from './ThemeSetup.js';
@@ -16,8 +17,12 @@ import '@fontsource/inter/800.css'; // Bolder
 
 export function FireflyRoot({sx, children, ctxProperties={}}) {
 
-    const customTheme = getAppOptions().theme?.customized?.();
+    const appOps= getAppOptions();
+    const customTheme = appOps.theme?.customized?.();
     const theme = extendTheme(customTheme || defaultTheme());
+    if (isDefined(appOps.showUserInfo)) { // the showUserInfo option will override the property default
+        ctxProperties= {...ctxProperties, showUserInfo:toBoolean(appOps.showUserInfo)};
+    }
 
     return (
         <AppPropertiesCtx.Provider value={ctxProperties}>