From b177b232a01e1a1fc12e2a8d972eb16419b8d57c Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Sat, 28 Dec 2024 00:53:11 +0300
Subject: [PATCH 01/34] bump SPC (0.1.92b3)

---
 package-lock.json | 659 ++++++++++++++++++++++++++++------------------
 package.json      |   2 +-
 2 files changed, 406 insertions(+), 255 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 30cd11f49a..86345732fe 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11,7 +11,7 @@
       "dependencies": {
         "@fortawesome/fontawesome-free": "^6.6.0",
         "@hms-dbmi-bgm/react-workflow-viz": "0.1.11",
-        "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.91",
+        "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.92b3",
         "@reduxjs/toolkit": "^2.2.6",
         "auth0-lock": "^12.5.1",
         "d3": "^7.5.0",
@@ -2644,8 +2644,8 @@
       }
     },
     "node_modules/@hms-dbmi-bgm/shared-portal-components": {
-      "version": "0.1.91",
-      "resolved": "git+ssh://git@github.com/4dn-dcic/shared-portal-components.git#4471b0d4602d1d302e7853252b7090030f146b6d",
+      "version": "0.1.92",
+      "resolved": "git+ssh://git@github.com/4dn-dcic/shared-portal-components.git#465b0a84066711176b107011b3fe7c3422a326ec",
       "license": "MIT",
       "dependencies": {
         "@4dn-dcic/react-infinite": "github:4dn-dcic/react-infinite#1.1.9",
@@ -7266,9 +7266,10 @@
       }
     },
     "node_modules/@turf/along/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/area": {
       "version": "6.5.0",
@@ -7321,9 +7322,10 @@
       }
     },
     "node_modules/@turf/bbox-polygon/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/bbox/node_modules/@turf/helpers": {
       "version": "7.1.0",
@@ -7350,9 +7352,10 @@
       }
     },
     "node_modules/@turf/bbox/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/bearing": {
       "version": "7.1.0",
@@ -7381,9 +7384,10 @@
       }
     },
     "node_modules/@turf/bearing/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/boolean-clockwise": {
       "version": "7.0.0",
@@ -7411,9 +7415,10 @@
       }
     },
     "node_modules/@turf/boolean-clockwise/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/boolean-contains": {
       "version": "6.5.0",
@@ -7606,9 +7611,10 @@
       }
     },
     "node_modules/@turf/buffer/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/buffer/node_modules/d3-array": {
       "version": "1.2.4",
@@ -7649,9 +7655,10 @@
       }
     },
     "node_modules/@turf/center/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/centroid": {
       "version": "6.5.0",
@@ -7691,9 +7698,10 @@
       }
     },
     "node_modules/@turf/circle/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/clone": {
       "version": "7.0.0",
@@ -7720,9 +7728,10 @@
       }
     },
     "node_modules/@turf/clone/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/destination": {
       "version": "7.1.0",
@@ -7751,9 +7760,10 @@
       }
     },
     "node_modules/@turf/destination/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/difference": {
       "version": "7.0.0",
@@ -7794,9 +7804,10 @@
       }
     },
     "node_modules/@turf/difference/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/distance": {
       "version": "7.1.0",
@@ -7825,9 +7836,10 @@
       }
     },
     "node_modules/@turf/distance/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/ellipse": {
       "version": "7.0.0",
@@ -7857,9 +7869,10 @@
       }
     },
     "node_modules/@turf/ellipse/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/helpers": {
       "version": "6.5.0",
@@ -7908,9 +7921,10 @@
       }
     },
     "node_modules/@turf/intersect/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/invariant": {
       "version": "7.1.0",
@@ -7938,9 +7952,10 @@
       }
     },
     "node_modules/@turf/invariant/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/jsts": {
       "version": "2.7.1",
@@ -8148,9 +8163,10 @@
       }
     },
     "node_modules/@turf/point-to-line-distance/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/polygon-to-line": {
       "version": "7.0.0",
@@ -8178,9 +8194,10 @@
       }
     },
     "node_modules/@turf/polygon-to-line/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/projection": {
       "version": "7.0.0",
@@ -8221,9 +8238,10 @@
       }
     },
     "node_modules/@turf/projection/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/rewind": {
       "version": "7.0.0",
@@ -8266,9 +8284,10 @@
       }
     },
     "node_modules/@turf/rewind/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/rhumb-bearing": {
       "version": "7.0.0",
@@ -8296,9 +8315,10 @@
       }
     },
     "node_modules/@turf/rhumb-bearing/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/rhumb-destination": {
       "version": "7.0.0",
@@ -8326,9 +8346,10 @@
       }
     },
     "node_modules/@turf/rhumb-destination/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
     "node_modules/@turf/rhumb-distance": {
       "version": "7.0.0",
@@ -8356,9 +8377,10 @@
       }
     },
     "node_modules/@turf/rhumb-distance/node_modules/@types/geojson": {
-      "version": "7946.0.14",
-      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz",
-      "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg=="
+      "version": "7946.0.15",
+      "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.15.tgz",
+      "integrity": "sha512-9oSxFzDCT2Rj6DfcHF8G++jxBKS7mBqXl5xrRW+Kbvjry6Uduya2iiwqHPhVXpasAVMBYKkEPGgKhd3+/HZ6xA==",
+      "license": "MIT"
     },
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+      "license": "MIT",
       "funding": {
         "type": "opencollective",
         "url": "https://opencollective.com/core-js"
@@ -31321,17 +31430,21 @@
       "integrity": "sha512-LwZrotdHOo12nQuZlHEmtuXdqGoOD0OhaxopaNFxWzInpEgaLWoVuAMbTzixuosCx2nEG58ngzW3vxdWoxIgdg=="
     },
     "node_modules/resolve": {
-      "version": "1.22.8",
-      "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.8.tgz",
-      "integrity": "sha512-oKWePCxqpd6FlLvGV1VU0x7bkPmmCNolxzjMf4NczoDnQcIWrAF+cPtZn5i6n+RfD2d9i0tzpKnG6Yk168yIyw==",
+      "version": "1.22.10",
+      "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.10.tgz",
+      "integrity": "sha512-NPRy+/ncIMeDlTAsuqwKIiferiawhefFJtkNSW0qZJEqMEb+qBt/77B/jGeeek+F0uOeN05CDa6HXbbIgtVX4w==",
+      "license": "MIT",
       "dependencies": {
-        "is-core-module": "^2.13.0",
+        "is-core-module": "^2.16.0",
         "path-parse": "^1.0.7",
         "supports-preserve-symlinks-flag": "^1.0.0"
       },
       "bin": {
         "resolve": "bin/resolve"
       },
+      "engines": {
+        "node": ">= 0.4"
+      },
       "funding": {
         "url": "https://github.com/sponsors/ljharb"
       }
@@ -32766,9 +32879,10 @@
       }
     },
     "node_modules/superagent/node_modules/form-data": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.0.tgz",
-      "integrity": "sha512-ETEklSGi5t0QMZuiXoA/Q6vcnxcLQP5vdugSpuAyi6SVGi2clPPp+xgEhuMaHC+zGgn31Kd235W35f7Hykkaww==",
+      "version": "4.0.1",
+      "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.1.tgz",
+      "integrity": "sha512-tzN8e4TX8+kkxGPK8D5u0FNmjPUjw3lwC9lSLxxoB/+GtsJG91CO8bSWy73APlgAZzZbXEYZJuxjkHH2w+Ezhw==",
+      "license": "MIT",
       "dependencies": {
         "asynckit": "^0.4.0",
         "combined-stream": "^1.0.8",
@@ -32915,9 +33029,9 @@
       }
     },
     "node_modules/terser": {
-      "version": "5.34.1",
-      "resolved": "https://registry.npmjs.org/terser/-/terser-5.34.1.tgz",
-      "integrity": "sha512-FsJZ7iZLd/BXkz+4xrRTGJ26o/6VTjQytUk8b8OxkwcD2I+79VPJlz7qss1+zE7h8GNIScFqXcDyJ/KqBYZFVA==",
+      "version": "5.37.0",
+      "resolved": "https://registry.npmjs.org/terser/-/terser-5.37.0.tgz",
+      "integrity": "sha512-B8wRRkmre4ERucLM/uXx4MOV5cbnOlVAqUst+1+iLKPI0dOgFO28f84ptoQt9HEI537PMzfYa/d+GEPKTRXmYA==",
       "license": "BSD-2-Clause",
       "dependencies": {
         "@jridgewell/source-map": "^0.3.3",
@@ -32933,15 +33047,16 @@
       }
     },
     "node_modules/terser-webpack-plugin": {
-      "version": "5.3.10",
-      "resolved": "https://registry.npmjs.org/terser-webpack-plugin/-/terser-webpack-plugin-5.3.10.tgz",
-      "integrity": "sha512-BKFPWlPDndPs+NGGCr1U59t0XScL5317Y0UReNrHaw9/FwhPENlq6bfgs+4yPfyP51vqC1bQ4rp1EfXW5ZSH9w==",
+      "version": "5.3.11",
+      "resolved": "https://registry.npmjs.org/terser-webpack-plugin/-/terser-webpack-plugin-5.3.11.tgz",
+      "integrity": "sha512-RVCsMfuD0+cTt3EwX8hSl2Ks56EbFHWmhluwcqoPKtBnfjiT6olaq7PRIRfhyU8nnC2MrnDrBLfrD/RGE+cVXQ==",
+      "license": "MIT",
       "dependencies": {
-        "@jridgewell/trace-mapping": "^0.3.20",
+        "@jridgewell/trace-mapping": "^0.3.25",
         "jest-worker": "^27.4.5",
-        "schema-utils": "^3.1.1",
-        "serialize-javascript": "^6.0.1",
-        "terser": "^5.26.0"
+        "schema-utils": "^4.3.0",
+        "serialize-javascript": "^6.0.2",
+        "terser": "^5.31.1"
       },
       "engines": {
         "node": ">= 10.13.0"
@@ -32965,14 +33080,50 @@
         }
       }
     },
+    "node_modules/terser-webpack-plugin/node_modules/ajv": {
+      "version": "8.17.1",
+      "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.17.1.tgz",
+      "integrity": "sha512-B/gBuNg5SiMTrPkC+A2+cW0RszwxYmn6VYxB/inlBStS5nx6xHIt/ehKRhIMhqusl7a8LjQoZnjCs5vhwxOQ1g==",
+      "license": "MIT",
+      "dependencies": {
+        "fast-deep-equal": "^3.1.3",
+        "fast-uri": "^3.0.1",
+        "json-schema-traverse": "^1.0.0",
+        "require-from-string": "^2.0.2"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/epoberezkin"
+      }
+    },
+    "node_modules/terser-webpack-plugin/node_modules/ajv-keywords": {
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-5.1.0.tgz",
+      "integrity": "sha512-YCS/JNFAUyr5vAuhk1DWm1CBxRHW9LbJ2ozWeemrIqpbsqKjHVxYPyi5GC0rjZIT5JxJ3virVTS8wk4i/Z+krw==",
+      "license": "MIT",
+      "dependencies": {
+        "fast-deep-equal": "^3.1.3"
+      },
+      "peerDependencies": {
+        "ajv": "^8.8.2"
+      }
+    },
+    "node_modules/terser-webpack-plugin/node_modules/json-schema-traverse": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz",
+      "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug==",
+      "license": "MIT"
+    },
     "node_modules/terser-webpack-plugin/node_modules/schema-utils": {
-      "version": "3.3.0",
-      "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.3.0.tgz",
-      "integrity": "sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==",
+      "version": "4.3.0",
+      "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.3.0.tgz",
+      "integrity": "sha512-Gf9qqc58SpCA/xdziiHz35F4GNIWYWZrEshUc/G/r5BnLph6xpKuLeoJoQuj5WfBIx/eQLf+hmVPYHaxJu7V2g==",
+      "license": "MIT",
       "dependencies": {
-        "@types/json-schema": "^7.0.8",
-        "ajv": "^6.12.5",
-        "ajv-keywords": "^3.5.2"
+        "@types/json-schema": "^7.0.9",
+        "ajv": "^8.9.0",
+        "ajv-formats": "^2.1.1",
+        "ajv-keywords": "^5.1.0"
       },
       "engines": {
         "node": ">= 10.13.0"
@@ -33043,9 +33194,9 @@
       "integrity": "sha512-jLN68Dx5kyFHaePoXWPsCGW5qdyZQtLYHkxkg02/Mz6g0kYpDx4FyP6XfArhQdlOC4b8Mv+EMxPo/8La7Tzghg=="
     },
     "node_modules/three": {
-      "version": "0.169.0",
-      "resolved": "https://registry.npmjs.org/three/-/three-0.169.0.tgz",
-      "integrity": "sha512-Ed906MA3dR4TS5riErd4QBsRGPcx+HBDX2O5yYE5GqJeFQTPU+M56Va/f/Oph9X7uZo3W3o4l2ZhBZ6f6qUv0w==",
+      "version": "0.171.0",
+      "resolved": "https://registry.npmjs.org/three/-/three-0.171.0.tgz",
+      "integrity": "sha512-Y/lAXPaKZPcEdkKjh0JOAHVv8OOnv/NDJqm0wjfCzyQmfKxV7zvkwsnBgPBKTzJHToSOhRGQAGbPJObT59B/PQ==",
       "license": "MIT",
       "peer": true
     },
diff --git a/package.json b/package.json
index 9f0e7181c0..98f6396f89 100644
--- a/package.json
+++ b/package.json
@@ -107,7 +107,7 @@
   "dependencies": {
     "@fortawesome/fontawesome-free": "^6.6.0",
     "@hms-dbmi-bgm/react-workflow-viz": "0.1.11",
-    "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.91",
+    "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.92b3",
     "@reduxjs/toolkit": "^2.2.6",
     "auth0-lock": "^12.5.1",
     "d3": "^7.5.0",

From c204f496d720944674917772b2edc84d772e9d21 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Sat, 28 Dec 2024 00:55:25 +0300
Subject: [PATCH 02/34] add more interval options

---
 .../static-pages/StatisticsPageView.js        | 11 +++--
 .../components/StatisticsPageViewBody.js      | 41 +++++++++++--------
 2 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/src/encoded/static/components/static-pages/StatisticsPageView.js b/src/encoded/static/components/static-pages/StatisticsPageView.js
index 8da6bb7130..b4afc85c89 100644
--- a/src/encoded/static/components/static-pages/StatisticsPageView.js
+++ b/src/encoded/static/components/static-pages/StatisticsPageView.js
@@ -153,12 +153,15 @@ export default class StatisticsPageView extends React.PureComponent {
     renderUsageSection(){
         const { shouldReaggregate } = StatisticsPageView.viewOptions.usage;
         const groupByOptions = {
-            'monthly'   : <span>Previous 12 Months</span>,
-            'daily30'     : <span>Previous 30 Days</span>,
-            'daily60'     : <span>Previous 60 Days</span>
+            'daily:30': <span>Previous 30 Days</span>,
+            'daily:60': <span>Previous 60 Days</span>,
+            'monthly:6': <span>Previous 6 Months</span>,
+            'monthly:12': <span>Previous 12 Months</span>,
+            'monthly:18': <span>Previous 18 Months</span>,
+            'monthly:All': <span>All</span>
         };
         return (
-            <dynamicImports.GroupByController groupByOptions={groupByOptions} initialGroupBy="daily60">
+            <dynamicImports.GroupByController groupByOptions={groupByOptions} initialGroupBy="monthly:6">
                 <dynamicImports.UsageStatsViewController {..._.pick(this.props, 'session', 'windowWidth', 'href')}>
                     <dynamicImports.StatsChartViewAggregator {...{ shouldReaggregate }} aggregationsToChartData={dynamicImports.usageAggsToChartData}>
                         <dynamicImports.UsageStatsView />
diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index aed79a3822..3a919e91e2 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -9,10 +9,15 @@ import * as d3 from 'd3';
 import { sub, add, startOfMonth, startOfDay, endOfMonth, endOfDay, toDate, format as formatDate } from 'date-fns';
 import DropdownItem from 'react-bootstrap/esm/DropdownItem';
 import DropdownButton from 'react-bootstrap/esm/DropdownButton';
+import Modal from 'react-bootstrap/esm/Modal';
 
 import { Checkbox } from '@hms-dbmi-bgm/shared-portal-components/es/components/forms/components/Checkbox';
 import { console, ajax, analytics, logger } from '@hms-dbmi-bgm/shared-portal-components/es/components/util';
 import { navigate } from './../../util';
+import { Term } from './../../util/Schemas';
+import { ColumnCombiner, CustomColumnController, SortController } from '@hms-dbmi-bgm/shared-portal-components/es/components/browse/EmbeddedSearchView';
+import { ControlsAndResults } from '@hms-dbmi-bgm/shared-portal-components/es/components/browse/components/ControlsAndResults';
+import { ItemDetailList } from '@hms-dbmi-bgm/shared-portal-components/es/components/ui/ItemDetailList';
 import {
     StatsViewController, GroupByDropdown, ColorScaleProvider,
     AreaChart, AreaChartContainer, LoadingIcon, ErrorIcon, HorizontalD3ScaleLegend,
@@ -638,22 +643,26 @@ export const usageAggsToChartData = _.pick(aggregationsToChartData,
 
 export class UsageStatsViewController extends React.PureComponent {
 
-    static getSearchReqMomentsForTimePeriod(currentGroupBy = "daily60"){
+    static getSearchReqMomentsForTimePeriod(currentGroupBy = "daily:60") {
         let untilDate = new Date();
         let fromDate;
-        if (currentGroupBy === 'monthly'){ // 1 yr (12 mths)
-            untilDate = sub(startOfMonth(untilDate), { minutes: 1 }); // Last minute of previous month
-            fromDate = toDate(untilDate);
-            fromDate = sub(fromDate, { months: 12 }); // Go back 12 months
-        } else if (currentGroupBy === 'daily30'){ // 30 days
-            untilDate = sub(untilDate, { days: 1 });
-            fromDate = toDate(untilDate);
-            fromDate = sub(fromDate, { days: 30 }); // Go back 30 days
-        }else if (currentGroupBy === 'daily60'){ // 60 days
+
+        if (currentGroupBy.startsWith("daily:")) {
+            const days = parseInt(currentGroupBy.split(":")[1], 10); // Extract the number after 'daily:'
             untilDate = sub(untilDate, { days: 1 });
-            fromDate = toDate(untilDate);
-            fromDate = sub(fromDate, { days: 60 }); // Go back 60 days
+            fromDate = sub(untilDate, { days }); // Go back the specified number of days
+        } else if (currentGroupBy.startsWith("monthly:")) {
+            const [, months] = currentGroupBy.split(":");
+            if (months === "All") { // Special case for 'monthly:All'
+                fromDate = new Date("2018-08-01");
+                untilDate = sub(startOfMonth(untilDate), { minutes: 1 }); // Last minute of previous month
+            } else {
+                const numMonths = parseInt(months, 10); // Extract the number after 'monthly:'
+                untilDate = sub(startOfMonth(untilDate), { minutes: 1 }); // Last minute of previous month
+                fromDate = sub(untilDate, { months: numMonths }); // Go back the specified number of months
+            }
         }
+
         return { fromDate, untilDate };
     }
 
@@ -679,7 +688,7 @@ export class UsageStatsViewController extends React.PureComponent {
                     "for_date"
                 ];
 
-                const date_increment = currentGroupBy === 'monthly' ? 'monthly' : 'daily';
+                const date_increment = currentGroupBy.startsWith('monthly') ? 'monthly' : 'daily';
 
                 let uri = '/search/?type=TrackingItem&tracking_type=google_analytics&sort=-google_analytics.for_date&format=json';
 
@@ -914,15 +923,15 @@ export function UsageStatsView(props){
         // We want all charts to share the same x axis. Here we round to date boundary.
         // Minor issue is that file downloads are stored in UTC/GMT while analytics are in EST timezone..
         // TODO improve on this somehow, maybe pass prop to FileDownload chart re: timezone parsing of some sort.
-        if (currentGroupBy === 'daily30' || currentGroupBy === 'daily60') {
+        if (currentGroupBy.startsWith('daily:')) {
             fromDate = add(startOfDay(propFromDate), { minutes: 15 });
             untilDate = add(endOfDay(propUntilDate), { minutes: 45 });
             dateRoundInterval = 'day';
-        } else if (currentGroupBy === 'monthly') {
+        } else if (currentGroupBy.startsWith('monthly:')) {
             fromDate = endOfMonth(propFromDate); // Not rly needed.
             untilDate = sub(endOfMonth(propUntilDate), { days: 1 });
             dateRoundInterval = 'month';
-        } else if (currentGroupBy === 'yearly') { // Not yet implemented
+        } else if (currentGroupBy.startsWith('yearly')) { // Not yet implemented
             dateRoundInterval = 'year';
         }
         return {

From 103c1cee22c60c2c353b9b294a099f55130d33bd Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 00:10:32 +0300
Subject: [PATCH 03/34] bump version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c6b3adf99e..132a9f80d6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "fourfront".
 name = "encoded"
-version = "8.4.6"
+version = "8.5.0"
 description = "4DN-DCIC Fourfront"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From 92a7c8c1cc8f82ef186acb57e65ef7b40f981463 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 00:10:56 +0300
Subject: [PATCH 04/34] override table styles

---
 .../static/scss/encoded/modules/_charts.scss  | 30 ++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/src/encoded/static/scss/encoded/modules/_charts.scss b/src/encoded/static/scss/encoded/modules/_charts.scss
index 47953cf7a8..82abd6fbd7 100644
--- a/src/encoded/static/scss/encoded/modules/_charts.scss
+++ b/src/encoded/static/scss/encoded/modules/_charts.scss
@@ -1399,7 +1399,35 @@ $workflow-node-color-type-global-context: #ffb3b3;
             .dropdown .btn {
                 margin-top: 10px;
             }
-        }   
+        }
+
+        .chart-group h5 {
+            font-weight: 600 !important;
+        }
+
+        .search-view-controls-and-results {
+            .above-results-table-row {
+                .right-buttons button[data-tip="Sort multiple columns"],
+                .right-buttons button[data-tip="Configure visible columns"] {
+                    display: none;
+                }
+            }
+            .search-headers-column-block {
+                &[data-first-visible-column=true] {
+                    .column-title {
+                        color: #ffffff !important;
+                    }
+                }
+            }
+            .search-result-column-block[data-field="display_title"] {
+                padding-left: 0px !important;
+            }
+            .search-result-column-block {
+                .inner {
+                    height: 30px !important;
+                }
+            }
+        }
     }
 
 }

From 334e143c2d48df48e9a751943217f21fddfbfd84 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 00:12:09 +0300
Subject: [PATCH 05/34] add toggles for table and chart

---
 .../static/components/viz/AreaChart.js        | 98 +++++++++++++------
 1 file changed, 70 insertions(+), 28 deletions(-)

diff --git a/src/encoded/static/components/viz/AreaChart.js b/src/encoded/static/components/viz/AreaChart.js
index 18cc64a594..0dc293dd1a 100644
--- a/src/encoded/static/components/viz/AreaChart.js
+++ b/src/encoded/static/components/viz/AreaChart.js
@@ -130,12 +130,23 @@ export class StatsChartViewAggregator extends React.PureComponent {
         'aggregationsToChartData' : PropTypes.object.isRequired,
         'shouldReaggregate' : PropTypes.func,
         'cumulativeSum': PropTypes.bool,
+        'initialChartToggles': PropTypes.shape({
+            'chart': PropTypes.object,
+            'table': PropTypes.object,
+            'expanded': PropTypes.object
+        }),
         'children' : PropTypes.node.isRequired
     };
 
     constructor(props){
         super(props);
-        const { cumulativeSum = false } = props;
+        const {
+            cumulativeSum = false,
+            initialChartToggles = {
+                chart: {},
+                table: {},
+                expanded: {}
+            } } = props;
 
         this.getRefWidth = this.getRefWidth.bind(this);
         this.handleToggle = this.handleToggle.bind(this);
@@ -143,7 +154,7 @@ export class StatsChartViewAggregator extends React.PureComponent {
         this.handleToggleCumulativeSum = this.handleToggleCumulativeSum.bind(this);
         this.generateAggsToState = this.generateAggsToState.bind(this);
         this.state = _.extend(this.generateAggsToState(props, {}), {
-            'chartToggles' : {},
+            'chartToggles' : initialChartToggles,
             'smoothEdges' : false,
             'cumulativeSum': cumulativeSum
         });
@@ -188,12 +199,13 @@ export class StatsChartViewAggregator extends React.PureComponent {
         return this.elemRef && this.elemRef.current && this.elemRef.current.clientWidth;
     }
 
-    handleToggle(key, cb){
+    handleToggle(id, typeKey, callbackFunc){
         this.setState(function(currState){
-            var nextTogglesState = _.extend({}, currState.chartToggles);
-            nextTogglesState[key] = !(nextTogglesState[key]);
+            // deep clone
+            var nextTogglesState =JSON.parse(JSON.stringify(currState.chartToggles));
+            nextTogglesState[typeKey][id] = !(nextTogglesState[typeKey][id]);
             return { 'chartToggles' : nextTogglesState };
-        }, cb);
+        }, callbackFunc);
     }
 
     handleToggleSmoothEdges(smoothEdges, cb){
@@ -1262,11 +1274,18 @@ ErrorIcon.defaultProps = { 'children' : "Loading failed. Please try again later.
 
 export class AreaChartContainer extends React.Component {
 
-    static isExpanded(props){
-        const { windowWidth, chartToggles, id } = props;
-        const gridState = layout.responsiveGridState(windowWidth);
-        if (gridState && ['lg', 'xl', 'xxl'].indexOf(gridState) === -1) return false;
-        return !!((chartToggles || {})[id]);
+    static isToggled(props, typeKey){
+        const { windowWidth, chartToggles = {}, id } = props;
+
+        const value = chartToggles[typeKey][id];
+        switch(typeKey) {
+            case 'expanded':
+                const gridState = layout.responsiveGridState(windowWidth);
+                if (gridState && ['lg', 'xl', 'xxl'].indexOf(gridState) === -1) return false;
+                return !!value;
+            default:
+                return !!value
+        }
     }
 
     static defaultProps = {
@@ -1278,8 +1297,8 @@ export class AreaChartContainer extends React.Component {
     constructor(props){
         super(props);
         this.buttonSection = this.buttonSection.bind(this);
-        this.toggleExpanded = _.throttle(this.toggleExpanded.bind(this), 1000);
-        this.expandButton = this.expandButton.bind(this);
+        this.toggleExpanded = _.throttle(this.toggleButton.bind(this), 1000);
+        this.commonButtons = this.commonButtons.bind(this);
 
         this.elemRef = React.createRef();
     }
@@ -1296,7 +1315,7 @@ export class AreaChartContainer extends React.Component {
         const { defaultColSize, width } = this.props;
         if (
             !(typeof width === 'number' && width) &&
-            (pastProps.defaultColSize !== defaultColSize || AreaChartContainer.isExpanded(pastProps) !== AreaChartContainer.isExpanded(this.props))
+            (pastProps.defaultColSize !== defaultColSize || AreaChartContainer.isToggled(pastProps, 'expanded') !== AreaChartContainer.isToggled(this.props, 'expanded'))
         ){
             setTimeout(()=>{ // Update w. new width.
                 this.forceUpdate();
@@ -1304,33 +1323,56 @@ export class AreaChartContainer extends React.Component {
         }
     }
 
-    toggleExpanded(e){
+    toggleButton(e, typeKey){
         const { onToggle, id } = this.props;
-        return typeof onToggle === 'function' && id && onToggle(id);
+        return typeof onToggle === 'function' && id && onToggle(id, typeKey);
     }
 
     getRefWidth(){
         return this.elemRef && this.elemRef.current && this.elemRef.current.clientWidth;
     }
 
-    expandButton(){
-        const { windowWidth } = this.props;
+    commonButtons(){
+        const { windowWidth, id, hideChartButton = false, hideTableButton = false } = this.props;
+        const buttons = [];
+
+        if (!hideChartButton) {
+            const toggled = AreaChartContainer.isToggled(this.props, 'chart');
+            const className = "btn btn-sm me-05 " + (toggled ? "btn-primary" : "btn-outline-dark");
+            buttons.push(
+                <button type="button" className={className} onClick={(e) => this.toggleButton(e, 'chart')} data-tip="Toggle chart view" key={id + '_chart'}>
+                    <i className="icon icon-fw fas icon-chart-bar" />
+                </button>
+            );
+        }
+        if (!hideTableButton) {
+            const toggled = AreaChartContainer.isToggled(this.props, 'table');
+            const className = "btn btn-sm me-05 " + (toggled ? "btn-primary" : "btn-outline-dark");
+            buttons.push(
+                <button type="button" className={className} onClick={(e) => this.toggleButton(e, 'table')} data-tip="Toggle data table view" key={id + '_table'}>
+                    <i className="icon icon-fw fas icon-table" />
+                </button>
+            );
+        }
         const gridState = layout.responsiveGridState(windowWidth);
-        if (['xs', 'sm', 'md'].indexOf(gridState) > -1) return null;
-        const expanded = AreaChartContainer.isExpanded(this.props);
-        return (
-            <button type="button" className="btn btn-outline-dark btn-sm" onClick={this.toggleExpanded}>
-                <i className={"icon icon-fw fas icon-search-" + (expanded ? 'minus' : 'plus')}/>
-            </button>
-        );
+        if (['xs', 'sm', 'md'].indexOf(gridState) === -1) {
+            const toggled = AreaChartContainer.isToggled(this.props, 'expanded');
+            const className = "btn btn-sm me-05 " + (toggled ? "btn-primary" : "btn-outline-dark");
+            buttons.push(
+                <button type="button" className={className} onClick={(e) => this.toggleButton(e, 'expanded')} data-tip="Toggle full width" key={id + '_expanded'}>
+                    <i className="icon icon-fw fas icon-search-plus" />
+                </button>
+            );
+        }
+        return buttons;
     }
 
     buttonSection(){
         const { extraButtons } = this.props;
         return (
-            <div className="pull-right mt-07">
+            <div className="pull-right mt-05">
                 { extraButtons }
-                { this.expandButton() }
+                { this.commonButtons() }
             </div>
         );
     }
@@ -1338,7 +1380,7 @@ export class AreaChartContainer extends React.Component {
     render(){
         const { title, subTitle, children, width, defaultHeight, colorScale, chartMargin, updateColorStore, legend } = this.props;
 
-        const expanded = AreaChartContainer.isExpanded(this.props);
+        const expanded = AreaChartContainer.isToggled(this.props, 'expanded');
         const useWidth = width || this.getRefWidth();
         const chartInnerWidth = expanded ? useWidth * 3 : useWidth;
         const useHeight = expanded ? 500 : (defaultHeight || AreaChart.defaultProps.height);

From 18f6c0cd31b0f0d8edd574a85049ba89b02d6cca Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 00:12:32 +0300
Subject: [PATCH 06/34] initialize toggles

---
 .../components/static-pages/StatisticsPageView.js    | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/encoded/static/components/static-pages/StatisticsPageView.js b/src/encoded/static/components/static-pages/StatisticsPageView.js
index b4afc85c89..4bffbac0ff 100644
--- a/src/encoded/static/components/static-pages/StatisticsPageView.js
+++ b/src/encoded/static/components/static-pages/StatisticsPageView.js
@@ -160,10 +160,18 @@ export default class StatisticsPageView extends React.PureComponent {
             'monthly:18': <span>Previous 18 Months</span>,
             'monthly:All': <span>All</span>
         };
+        const dataKeys = _.keys(dynamicImports.usageAggsToChartData || {});
+        const initialChartToggles = {
+            'chart': dataKeys.reduce((acc, key) => { acc[key] = true; return acc; }, {}),
+            'table': dataKeys.reduce((acc, key) => { acc[key] = true; return acc; }, {}),
+            'expanded': dataKeys.reduce((acc, key) => { acc[key] = false; return acc; }, {})
+        };
+        // override
+        initialChartToggles.table['fields_faceted'] = false;
         return (
-            <dynamicImports.GroupByController groupByOptions={groupByOptions} initialGroupBy="monthly:6">
+            <dynamicImports.GroupByController groupByOptions={groupByOptions} initialGroupBy="daily:60">
                 <dynamicImports.UsageStatsViewController {..._.pick(this.props, 'session', 'windowWidth', 'href')}>
-                    <dynamicImports.StatsChartViewAggregator {...{ shouldReaggregate }} aggregationsToChartData={dynamicImports.usageAggsToChartData}>
+                    <dynamicImports.StatsChartViewAggregator {...{ shouldReaggregate }} aggregationsToChartData={dynamicImports.usageAggsToChartData} initialChartToggles={initialChartToggles}>
                         <dynamicImports.UsageStatsView />
                     </dynamicImports.StatsChartViewAggregator>
                 </dynamicImports.UsageStatsViewController>

From 6ec676661822b8abb30a1f7f063f77c8fd00241d Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 00:13:00 +0300
Subject: [PATCH 07/34] add statistics table and tracking item viewer

---
 .../components/StatisticsPageViewBody.js      | 339 +++++++++++++++++-
 1 file changed, 324 insertions(+), 15 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 3a919e91e2..5a7229ea96 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -1,6 +1,6 @@
 'use strict';
 
-import React, { useMemo } from 'react';
+import React, { useMemo, useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import _ from 'underscore';
 import memoize from 'memoize-one';
@@ -248,7 +248,7 @@ export const commonParsingFxn = {
             const { google_analytics : {
                 reports : {
                     [reportName] : currentReport = []
-                }, // `currentReport` => List of JSON objects (report entries, 1 per unique dimension value) - Note: 1 per unique dimension may not be valid for post processing report items in smaht-foursight 
+                }, // `currentReport` => List of JSON objects (report entries, 1 per unique dimension value) - Note: 1 per unique dimension may not be valid for post processing report items in smaht-foursight
                 for_date
             } } = trackingItem;
 
@@ -272,7 +272,7 @@ export const commonParsingFxn = {
                     termsInAllItems.add(term);
                     termsInCurrenItem.add(term);
                 }
-                totalSessions += trackingItemItem[countKey]
+                totalSessions += trackingItemItem[countKey];
                 return { groupedTermsObj, totalSessions };
             }, { groupedTermsObj: {}, totalSessions: 0 });
 
@@ -901,7 +901,7 @@ class UsageChartsCountByDropdown extends React.PureComponent {
 
 export function UsageStatsView(props){
     const {
-        loadingStatus, mounted, session, groupByOptions, handleGroupByChange, currentGroupBy, windowWidth,
+        loadingStatus, mounted, href, session, schemas, groupByOptions, handleGroupByChange, currentGroupBy, windowWidth,
         changeCountByForChart, countBy,
         // Passed in from StatsChartViewAggregator:
         sessions_by_country, chartToggles, fields_faceted, /* fields_faceted_group_by, browse_search_queries, other_search_queries, */
@@ -917,6 +917,8 @@ export function UsageStatsView(props){
         return <div className="stats-charts-container" key="charts" id="usage"><LoadingIcon/></div>;
     }
 
+    const [transposed, setTransposed] = useState(true);
+    const [hideEmptyColumns, setHideEmptyColumns] = useState(true);
     const { anyExpandedCharts, commonXDomain, dateRoundInterval } = useMemo(function(){
         const { fromDate: propFromDate, untilDate: propUntilDate } = UsageStatsViewController.getSearchReqMomentsForTimePeriod(currentGroupBy);
         let fromDate, untilDate, dateRoundInterval;
@@ -935,7 +937,7 @@ export function UsageStatsView(props){
             dateRoundInterval = 'year';
         }
         return {
-            anyExpandedCharts: _.any(_.values(chartToggles)),
+            anyExpandedCharts: _.any(_.values(chartToggles.expanded || {})),
             commonXDomain: [fromDate, untilDate],
             dateRoundInterval
         };
@@ -953,16 +955,25 @@ export function UsageStatsView(props){
     const enableFileDownloadsChartTooltipItemClick = (countBy.file_downloads === 'top_files');
     const fileDownloadsChartHeight = enableFileDownloadsChartTooltipItemClick ? 350 : commonContainerProps.defaultHeight;
 
+    const isSticky = true; //!_.any(_.values(tableToggle), (v)=> v === true);
+    const commonTableProps = { windowWidth, href, session, schemas, transposed, dateRoundInterval, cumulativeSum, hideEmptyColumns, chartToggles };
+
     return (
         <div className="stats-charts-container" key="charts" id="usage">
 
             <GroupByDropdown {...{ groupByOptions, loadingStatus, handleGroupByChange, currentGroupBy }}
-                title="Show" outerClassName="dropdown-container mb-0 sticky-top">
+                title="Show" outerClassName={"dropdown-container mb-0" + (isSticky ? " sticky-top" : "")}>
                 <div className="d-inline-block ms-15 me-15">
-                    <Checkbox checked={smoothEdges} onChange={onSmoothEdgeToggle}>Smooth Edges</Checkbox>
+                    <Checkbox checked={smoothEdges} onChange={onSmoothEdgeToggle} data-tip="Toggle between smooth/sharp edges">Smooth Edges</Checkbox>
+                </div>
+                <div className="d-inline-block me-15">
+                    <Checkbox checked={cumulativeSum} onChange={onCumulativeSumToggle} data-tip="Show as cumulative sum">Cumulative Sum</Checkbox>
+                </div>
+                <div className="d-inline-block me-15">
+                    <Checkbox checked={transposed} onChange={() => setTransposed(!transposed)} data-tip="Transpose data table">Transpose Data</Checkbox>
                 </div>
                 <div className="d-inline-block">
-                    <Checkbox checked={cumulativeSum} onChange={onCumulativeSumToggle}>Show as cumulative sum</Checkbox>
+                    <Checkbox checked={hideEmptyColumns} onChange={() => setHideEmptyColumns(!hideEmptyColumns)} data-tip="Hide empty data table columns">Hide Empty Columns</Checkbox>
                 </div>
             </GroupByDropdown>
 
@@ -986,15 +997,34 @@ export function UsageStatsView(props){
                     <AreaChartContainer {...commonContainerProps} id="file_downloads" defaultHeight={fileDownloadsChartHeight}
                         title={<h5 className="text-400 mt-0">Total File Count</h5>}
                         subTitle={enableFileDownloadsChartTooltipItemClick && <h4 className="fw-normal text-secondary">Click bar to view details</h4>}>
-                        <AreaChart {...commonChartProps} data={file_downloads} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} />
+                        {chartToggles.chart?.file_downloads ?
+                            <AreaChart {...commonChartProps} data={file_downloads} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} />
+                            : <React.Fragment />}
                     </AreaChartContainer>
 
+                    {chartToggles.table?.file_downloads &&
+                        <StatisticsTable data={file_downloads}
+                            key={'dt_file_downloads'}
+                            {...commonTableProps}
+                            containerId="content_file_downloads" />
+                    }
+
                     <AreaChartContainer {...commonContainerProps} id="file_downloads_volume" defaultHeight={fileDownloadsChartHeight}
                         title={<h5 className="text-400 mt-0">Total File Size (GB)</h5>}
                         subTitle={enableFileDownloadsChartTooltipItemClick && <h4 className="fw-normal text-secondary">Click bar to view details</h4>}>
-                        <AreaChart {...commonChartProps} data={file_downloads_volume} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} yAxisLabel="GB" />
+                        {chartToggles.chart?.file_downloads_volume ?
+                            <AreaChart {...commonChartProps} data={file_downloads_volume} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} yAxisLabel="GB" />
+                            : <React.Fragment />}
                     </AreaChartContainer>
 
+                    {chartToggles.table?.file_downloads_volume &&
+                        <StatisticsTable data={file_downloads_volume}
+                            key={'dt_file_downloads_volume'}
+                            valueLabel="GB"
+                            {...commonTableProps}
+                            containerId="content_file_downloads_volume" />
+                    }
+
                     <p className="fst-italic mt-2">Download tracking started in August 2018 | Re-Implemented in Feb 2020 and August 2023</p>
 
                 </ColorScaleProvider>
@@ -1016,9 +1046,18 @@ export function UsageStatsView(props){
                         }
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="file_views" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
-                        <AreaChart {...commonChartProps} data={file_views} />
+                        {chartToggles.chart?.file_views ?
+                            <AreaChart {...commonChartProps} data={file_views} />
+                            : <React.Fragment />}
                     </AreaChartContainer>
 
+                    {chartToggles.table?.file_views &&
+                        <StatisticsTable data={file_views}
+                            key={'dt_file_views'}
+                            {...commonTableProps}
+                            containerId="content_file_views" />
+                    }
+
                 </ColorScaleProvider>
 
                 : null}
@@ -1037,9 +1076,18 @@ export function UsageStatsView(props){
                         }
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="sessions_by_country" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
-                        <AreaChart {...commonChartProps} data={sessions_by_country} />
+                        {chartToggles.chart?.sessions_by_country ?
+                            <AreaChart {...commonChartProps} data={sessions_by_country} />
+                            : <React.Fragment />}
                     </AreaChartContainer>
 
+                    {chartToggles.table?.sessions_by_country &&
+                        <StatisticsTable data={sessions_by_country}
+                            key={'dt_sessions_by_country'}
+                            {...commonTableProps}
+                            containerId="content_sessions_by_country" />
+                    }
+
 
                 </ColorScaleProvider>
 
@@ -1089,9 +1137,18 @@ export function UsageStatsView(props){
                         }
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="experiment_set_views" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
-                        <AreaChart {...commonChartProps} data={experiment_set_views} />
+                        {chartToggles.chart?.experiment_set_views ?
+                            <AreaChart {...commonChartProps} data={experiment_set_views} />
+                            : <React.Fragment />}
                     </AreaChartContainer>
 
+                    {chartToggles.table?.experiment_set_views &&
+                        <StatisticsTable data={experiment_set_views}
+                            key={'dt_experiment_set_views'}
+                            {...commonTableProps}
+                            containerId="content_experiment_set_views" />
+                    }
+
                 </ColorScaleProvider>
 
                 : null }
@@ -1110,9 +1167,18 @@ export function UsageStatsView(props){
                         }
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="fields_faceted" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
-                        <AreaChart {...commonChartProps} data={fields_faceted} />
+                        {chartToggles.chart?.fields_faceted ?
+                            <AreaChart {...commonChartProps} data={fields_faceted} />
+                            : <React.Fragment />}
                     </AreaChartContainer>
 
+                    {chartToggles.table?.fields_faceted &&
+                        <StatisticsTable data={fields_faceted}
+                            key={'dt_fields_faceted'}
+                            {...commonTableProps}
+                            containerId="content_fields_faceted" />
+                    }
+
                 </ColorScaleProvider>
 
                 : null }
@@ -1393,4 +1459,247 @@ const ChartSubTitle = memoize(function ({ data, invalidDateRange }) {
         return <h4 className="fw-normal text-secondary">No data to display</h4>;
     }
     return null;
-});
\ No newline at end of file
+});
+
+/**
+ * converts aggregates to SearchView-compatible context objects and displays in table
+ */
+const StatisticsTable = React.memo((props) => {
+    const {
+        data, valueLabel = null, session, schemas, containerId = '',
+        href, dateRoundInterval,  transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
+        limit = 0, excludeNones = false // limit and excludeNones are evaluated for only transposed data
+    } = props;
+    const [columns, setColumns] = useState({});
+    const [columnDefinitions, setColumnDefinitions] = useState([]);
+    const [graph, setGraph] = useState([]);
+    const [showModal, setShowModal] = useState(false);
+    const [modalForDate, setModalForDate] = useState();
+
+    const transposeData = (data) => {
+        const result = [];
+        const termMap = {};
+
+        data.forEach(({ date, children }) => {
+            children.forEach(({ term, count, total }) => {
+                // remove None-like values
+                if (excludeNones && ['N/A', 'None', '(not set)'].indexOf(term) !== -1) {
+                    return;
+                }
+
+                if (!termMap[term]) {
+                    termMap[term] = { term, count: 0, total: 0, children: [] };
+                    result.push(termMap[term]);
+                }
+
+                termMap[term].children.push({ date, count, total });
+                termMap[term].count += count;
+                termMap[term].total += total;
+            });
+        });
+
+        return _.sortBy(result, (r) => -r.total);
+    };
+
+    const roundValue = function (value, label, threshold = 0.01) {
+        if (value === 0) return value;
+        const roundedValue = (value >= threshold && value % 1 > 0) ? Math.round(value * 100) / 100 : (value >= threshold ? value : ('<' + threshold));
+        return label ? roundedValue + ' ' + label : roundedValue;
+    };
+
+    useEffect(() => {
+        if (!Array.isArray(data) || data.length === 0) {
+            return;
+        }
+
+        const processData = transposed ? transposeData(data).slice(0, limit > 0 ? limit : undefined) : data;
+
+        // date or term column based on transposed or not
+        let cols = {
+            'display_title': {
+                title: transposed ? 'Term' : 'Date',
+                type: 'string',
+                noSort: true,
+                widthMap: transposed ? { 'lg': 250, 'md': 200, 'sm': 200 } : { 'lg': 200, 'md': 200, 'sm': 200 },
+                render: function (result) {
+                    // overall sum
+                    const overallSum = roundValue(result.overall_sum || 0, valueLabel);
+                    const tooltip = `${result.display_title} (${overallSum})`;
+
+                    return transposed ? (
+                        <span className="value text-truncate text-start" data-tip={tooltip.length > 40 ? tooltip : null}>
+                            {result.display_title} <strong>({overallSum})</strong>
+                        </span>
+                    ) : (
+                        <a href="#"
+                            onClick={(e) => {
+                                setModalForDate(result.display_title);
+                                setShowModal(true);
+                                e.preventDefault();
+                            }}
+                            data-tip="Show details">
+                            {result.display_title} <strong>({overallSum})</strong>
+                        </a>
+                    );
+                }
+            }
+        };
+
+        // Function to check a vertical slice (column)
+        const hasNonZeroInColumn = (arrays, columnIndex) => _.any(arrays, (row) => row.children[columnIndex].count !== 0);
+
+        // create columns and columnExtensionMap
+        const [item] = processData;
+        if (item && Array.isArray(item.children) && item.children.length > 0) {
+            const keys = transposed ? _.pluck(item.children, 'date') : _.pluck(item.children, 'term');
+            cols = _.reduce(keys, (memo, dataKey, index) => {
+                if (hideEmptyColumns && !hasNonZeroInColumn(processData, index)) {
+                    return memo;
+                }
+                memo[dataKey] = {
+                    title: dataKey,
+                    type: 'integer',
+                    noSort: true,
+                    widthMap: { 'lg': 140, 'md': 120, 'sm': 120 },
+                    render: function (result) {
+                        if (result[dataKey] !== 0) {
+                            return (
+                                <a href="#"
+                                    onClick={(e) => {
+                                        setModalForDate(transposed ? dataKey : result.display_title);
+                                        setShowModal(true);
+                                        e.preventDefault();
+                                    }}
+                                    data-tip="Show details"
+                                    className="value text-end fw-bold">
+                                    {roundValue(result[dataKey], valueLabel)}
+                                </a>
+                            );
+                        } else {
+                            return (<span className="value text-end">0</span>);
+                        }
+                    }
+                };
+                return memo;
+            }, { ...cols });
+        }
+
+        setColumns(cols);
+        const colDefs = _.map(_.pairs(cols), function (p) { return { field: p[0], ...p[1] } });
+        setColumnDefinitions(colDefs);
+
+        // create @graph
+        const result = _.map(processData, function (d) {
+            return {
+                display_title: transposed ? (d.termDisplayAs || d.term) : d.date,
+                '@id': transposed ? d.term : d.date,
+                ..._.reduce(d.children, (memo2, c) => {
+                    memo2[transposed ? c.date : c.term] = c.count;
+                    return memo2;
+                }, {}),
+                '@type': ['Item'],
+                'overall_sum': !cumulativeSum ? (d.total || 0) : _.reduce(d.children, (memo, c) => memo + c.count, 0),
+                'date_created': transposed ? d.term : d.date
+            };
+        });
+        setGraph(result);
+    }, [data, transposed, hideEmptyColumns]);
+
+    const passProps = {
+        isFullscreen: false,
+        href,
+        context: {
+            '@graph': graph || [],
+            total: graph?.length || 0,
+            columns: columns || [],
+            facets: null
+        },
+        results: graph || [],
+        columns,
+        columnExtensionMap: columns,
+        columnDefinitions: columnDefinitions,
+        session,
+        maxHeight: 500,
+        maxResultsBodyHeight: 500,
+        tableColumnClassName: "col-12",
+        facetColumnClassName: "d-none",
+        defaultColAlignment: "text-end",
+        stickyFirstColumn: true,
+        isOwnPage: false,
+        termTransformFxn: Term.toName
+    };
+
+    const modalProps = {
+        ...{ dateRoundInterval, schemas },
+        forDate: modalForDate,
+        onTrackingItemViewerCancel: () => setShowModal(false)
+    };
+
+    return (
+        <React.Fragment>
+            <div className="container" id={containerId}>
+                <CustomColumnController {...{ windowWidth }} hiddenColumns={{}} columnDefinitions={columnDefinitions} context={passProps.context}>
+                    <SortController>
+                        <ControlsAndResults {...passProps} />
+                    </SortController>
+                </CustomColumnController>
+            </div>
+            {showModal && <TrackingItemViewer {...modalProps} />}
+        </React.Fragment>
+    );
+});
+
+/**
+ * displays relevant tracking item (fetched via ajax call) in item detail list
+ */
+const TrackingItemViewer = React.memo(function (props) {
+    const { schemas, forDate, dateRoundInterval='day', reportName, onTrackingItemViewerCancel } = props;
+
+    const [isLoading, setIsLoading] = useState(true);
+    const [trackingItem, setTrackingItem] = useState();
+    const dateIncrement = (dateRoundInterval === 'month') ? 'monthly' : 'daily';
+    const href=`/search/?type=TrackingItem&google_analytics.for_date=${forDate}&google_analytics.date_increment=${dateIncrement}`;
+
+    useEffect(() => {
+        ajax.load(
+            href,
+            (resp) => {
+                const graph = resp['@graph'] || [];
+                setTrackingItem(graph.length > 0 ? graph[0] : null);
+                setIsLoading(false);
+            },
+            'GET',
+            (err) => {
+                Alerts.queue({
+                    title: 'Fetching tracking items failed',
+                    message:
+                        'Check your internet connection or if you have been logged out due to expired session.',
+                    style: 'danger',
+                });
+                setIsLoading(false);
+            }
+        );
+    }, [forDate, dateRoundInterval, reportName]);
+
+    return (
+        <Modal show size="xl" onHide={onTrackingItemViewerCancel} className="tracking-item-viewer">
+            <Modal.Header closeButton>
+                <Modal.Title>{forDate}</Modal.Title>
+            </Modal.Header>
+            <Modal.Body>
+                {isLoading ?
+                    <span className="pull-right">
+                        <i className="account-icon icon icon-spin icon-circle-notch fas align-middle" />
+                    </span> :
+                    <ItemDetailList context={trackingItem} collapsed={false} schemas={schemas} />
+                }
+            </Modal.Body>
+        </Modal>
+    );
+});
+TrackingItemViewer.propTypes = {
+    forDate: PropTypes.string.isRequired,
+    dateRoundInterval: PropTypes.oneOf(['daily', 'monthly']),
+    onTrackingItemViewerCancel: PropTypes.func.isRequired,
+    schemas: PropTypes.object
+};
\ No newline at end of file

From e9aea3802da5a1298b9e6df17c1c222067a59043 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 13:04:55 +0300
Subject: [PATCH 08/34] add y-axis scale

---
 .../components/StatisticsPageViewBody.js      | 58 ++++++++++++++++---
 .../static/components/viz/AreaChart.js        |  4 +-
 2 files changed, 54 insertions(+), 8 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 5a7229ea96..b1a42ce770 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -919,6 +919,7 @@ export function UsageStatsView(props){
 
     const [transposed, setTransposed] = useState(true);
     const [hideEmptyColumns, setHideEmptyColumns] = useState(true);
+    const [ scale, setScale ] = useState({ yAxisScale: 'Pow', yAxisPower: 0.7 });
     const { anyExpandedCharts, commonXDomain, dateRoundInterval } = useMemo(function(){
         const { fromDate: propFromDate, untilDate: propUntilDate } = UsageStatsViewController.getSearchReqMomentsForTimePeriod(currentGroupBy);
         let fromDate, untilDate, dateRoundInterval;
@@ -955,6 +956,8 @@ export function UsageStatsView(props){
     const enableFileDownloadsChartTooltipItemClick = (countBy.file_downloads === 'top_files');
     const fileDownloadsChartHeight = enableFileDownloadsChartTooltipItemClick ? 350 : commonContainerProps.defaultHeight;
 
+    const { showScaleRange, scaleRangeTooltip, scaleRangeMin, scaleRangeMax, scaleRangeStep } = UsageStatsView.getYScaleDefaults(scale['yAxisScale']);
+
     const isSticky = true; //!_.any(_.values(tableToggle), (v)=> v === true);
     const commonTableProps = { windowWidth, href, session, schemas, transposed, dateRoundInterval, cumulativeSum, hideEmptyColumns, chartToggles };
 
@@ -972,9 +975,29 @@ export function UsageStatsView(props){
                 <div className="d-inline-block me-15">
                     <Checkbox checked={transposed} onChange={() => setTransposed(!transposed)} data-tip="Transpose data table">Transpose Data</Checkbox>
                 </div>
-                <div className="d-inline-block">
+                <div className="d-inline-block me-15">
                     <Checkbox checked={hideEmptyColumns} onChange={() => setHideEmptyColumns(!hideEmptyColumns)} data-tip="Hide empty data table columns">Hide Empty Columns</Checkbox>
                 </div>
+                <div className="d-inline-block mt-06">
+                    <div className="d-md-flex">
+                        <span className="text-500 me-1">Y-Axis scale:</span>
+                        <div className="me-05">
+                            <DropdownButton size="sm"
+                                title={(scale && scale['yAxisScale'] && UsageStatsView.yScaleLabels[scale['yAxisScale']]) || '-'}
+                                onSelect={(e) => setScale({ yAxisScale: e, yAxisPower: e === 'Pow' ? 0.5 : 50 })}>
+                                <DropdownItem eventKey={'Linear'} key={'scale-linear'} >{UsageStatsView.yScaleLabels['Linear']}</DropdownItem>
+                                <DropdownItem eventKey={'Pow'} key={'scale-pow'} >{UsageStatsView.yScaleLabels['Pow']}</DropdownItem>
+                                <DropdownItem eventKey={'Symlog'} key={'scale-log'} >{UsageStatsView.yScaleLabels['Symlog']}</DropdownItem>
+                            </DropdownButton>
+                        </div>
+                        <div className={"ms-md-15" + (showScaleRange ? " d-block d-md-inline-block" : " d-none")}>
+                            <input type="range" id="input_range_y_scale_power" className="w-75"
+                                min={scaleRangeMin} max={scaleRangeMax} step={scaleRangeStep} value={scale['yAxisPower']} data-tip={scaleRangeTooltip}
+                                onChange={(e) => setScale({ yAxisScale: scale['yAxisScale'], yAxisPower: e.target.valueAsNumber })} />
+                            <span className="ms-05">{scale['yAxisPower']}</span>
+                        </div>
+                    </div>
+                </div>
             </GroupByDropdown>
 
             { session && file_downloads ?
@@ -998,7 +1021,7 @@ export function UsageStatsView(props){
                         title={<h5 className="text-400 mt-0">Total File Count</h5>}
                         subTitle={enableFileDownloadsChartTooltipItemClick && <h4 className="fw-normal text-secondary">Click bar to view details</h4>}>
                         {chartToggles.chart?.file_downloads ?
-                            <AreaChart {...commonChartProps} data={file_downloads} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} />
+                            <AreaChart {...commonChartProps} data={file_downloads} {...scale} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1013,7 +1036,7 @@ export function UsageStatsView(props){
                         title={<h5 className="text-400 mt-0">Total File Size (GB)</h5>}
                         subTitle={enableFileDownloadsChartTooltipItemClick && <h4 className="fw-normal text-secondary">Click bar to view details</h4>}>
                         {chartToggles.chart?.file_downloads_volume ?
-                            <AreaChart {...commonChartProps} data={file_downloads_volume} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} yAxisLabel="GB" />
+                            <AreaChart {...commonChartProps} data={file_downloads_volume} {...scale} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} yAxisLabel="GB" />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1047,7 +1070,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="file_views" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.file_views ?
-                            <AreaChart {...commonChartProps} data={file_views} />
+                            <AreaChart {...commonChartProps} data={file_views} {...scale} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1077,7 +1100,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="sessions_by_country" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.sessions_by_country ?
-                            <AreaChart {...commonChartProps} data={sessions_by_country} />
+                            <AreaChart {...commonChartProps} data={sessions_by_country} {...scale} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1138,7 +1161,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="experiment_set_views" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.experiment_set_views ?
-                            <AreaChart {...commonChartProps} data={experiment_set_views} />
+                            <AreaChart {...commonChartProps} data={experiment_set_views} {...scale} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1168,7 +1191,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="fields_faceted" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.fields_faceted ?
-                            <AreaChart {...commonChartProps} data={fields_faceted} />
+                            <AreaChart {...commonChartProps} data={fields_faceted} {...scale} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1213,6 +1236,27 @@ UsageStatsView.titleExtensions = {
         'sessions': 'by unique users'
     }
 };
+UsageStatsView.getYScaleDefaults = function (yScale) {
+    let showScaleRange = true;
+    let scaleRangeTooltip = '';
+    let scaleRangeMin, scaleRangeMax, scaleRangeStep;
+    //set defaults
+    if (yScale === 'Pow') {
+        scaleRangeMin = 0; scaleRangeMax = 1; scaleRangeStep = 0.1;
+        scaleRangeTooltip = 'exponent';
+    } else if (yScale === 'Symlog') {
+        scaleRangeMin = 0; scaleRangeMax = 100; scaleRangeStep = 0.5;
+        scaleRangeTooltip = 'constant';
+    } else {
+        showScaleRange = false;
+    }
+    return { showScaleRange, scaleRangeTooltip, scaleRangeMin, scaleRangeMax, scaleRangeStep };
+};
+UsageStatsView.yScaleLabels = {
+    'Linear': 'Linear',
+    'Symlog': 'Log',
+    'Pow': 'Pow'
+};
 
 
 export function SubmissionsStatsView(props) {
diff --git a/src/encoded/static/components/viz/AreaChart.js b/src/encoded/static/components/viz/AreaChart.js
index 0dc293dd1a..a1d6bc3a9c 100644
--- a/src/encoded/static/components/viz/AreaChart.js
+++ b/src/encoded/static/components/viz/AreaChart.js
@@ -767,7 +767,7 @@ export class AreaChart extends React.PureComponent {
         'stackChildren'         : true,
         'height'                : 300,
         'yAxisLabel'            : 'Count',
-        'yAxisScale'            : 'Linear', // Must be one of 'Linear', 'Log', 'Pow'
+        'yAxisScale'            : 'Pow', // Must be one of 'Linear', 'Log', 'Pow'
         'yAxisPower'            : null,
         'xDomain'               : [ new Date('2017-03-01'), null ],
         'yDomain'               : [ 0, null ],
@@ -909,6 +909,8 @@ export class AreaChart extends React.PureComponent {
         const scale = d3['scale' + yAxisScale]().rangeRound([height, 0]).domain(yExtents);
         if (yAxisScale === 'Pow' && yAxisPower !== null){
             scale.exponent(yAxisPower);
+        } else if (yAxisScale === 'Symlog' && yAxisPower !== null){
+            scale.constant(yAxisPower);
         }
         return scale;
     }

From b6bb816febaddea35325ec9d684761645bf00c17 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 13:30:24 +0300
Subject: [PATCH 09/34] override rowHeight

---
 .../static-pages/components/StatisticsPageViewBody.js         | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index b1a42ce770..a58eebc2ad 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -1512,7 +1512,8 @@ const StatisticsTable = React.memo((props) => {
     const {
         data, valueLabel = null, session, schemas, containerId = '',
         href, dateRoundInterval,  transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
-        limit = 0, excludeNones = false // limit and excludeNones are evaluated for only transposed data
+        limit = 0, excludeNones = false, // limit and excludeNones are evaluated for only transposed data
+        rowHeight = 31
     } = props;
     const [columns, setColumns] = useState({});
     const [columnDefinitions, setColumnDefinitions] = useState([]);
@@ -1665,6 +1666,7 @@ const StatisticsTable = React.memo((props) => {
         session,
         maxHeight: 500,
         maxResultsBodyHeight: 500,
+        rowHeight,
         tableColumnClassName: "col-12",
         facetColumnClassName: "d-none",
         defaultColAlignment: "text-end",

From 87b70d866db69cd7153c7250141ef330157340e7 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 16:39:13 +0300
Subject: [PATCH 10/34] filter zero rows and fix top files

---
 .../components/StatisticsPageViewBody.js      | 68 +++++++++++++------
 1 file changed, 49 insertions(+), 19 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index a58eebc2ad..38d52fa5de 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -232,7 +232,7 @@ export const commonParsingFxn = {
 
         return aggsList;
     },
-    'analytics_to_buckets' : function(resp, reportName, termBucketField, countKey, cumulativeSum, topCount = 0){
+    'analytics_to_buckets' : function(resp, reportName, termBucketField, countKey, cumulativeSum, termDisplayAsFunc = null, topCount = 0){
         const termsInAllItems = new Set();
 
         // De-dupe -- not particularly necessary as D3 handles this, however nice to have well-formatted data.
@@ -248,7 +248,7 @@ export const commonParsingFxn = {
             const { google_analytics : {
                 reports : {
                     [reportName] : currentReport = []
-                }, // `currentReport` => List of JSON objects (report entries, 1 per unique dimension value) - Note: 1 per unique dimension may not be valid for post processing report items in smaht-foursight
+                } = {}, // `currentReport` => List of JSON objects (report entries, 1 per unique dimension value) - Note: 1 per unique dimension may not be valid for post processing report items in smaht-foursight 
                 for_date
             } } = trackingItem;
 
@@ -265,6 +265,7 @@ export const commonParsingFxn = {
                 } else {
                     groupedTermsObj[term] = {
                         'term': term,
+                        'termDisplayAs': typeof termDisplayAsFunc === 'function' ? termDisplayAsFunc(trackingItemItem) : null,
                         'count': trackingItemItem[countKey],
                         'total': trackingItemItem[countKey],
                         'date': for_date
@@ -287,7 +288,7 @@ export const commonParsingFxn = {
                     if (cumulativeSum) {
                         let { count = 0, total = 0 } = termTotals[termItem.term] || {};
                         total += (termItem.total || 0);
-                        count += (termItem.count || 0);
+                        count = (termItem.count || 0);
                         termTotals[termItem.term] = { total, count };
 
                         cloned.count = count;
@@ -303,7 +304,8 @@ export const commonParsingFxn = {
                     if (!termsInCurrenItem.has(term)) {
                         currentItem.children.push({
                             'term': term,
-                            'count': termTotals[term].count,
+                            'termDisplayAs': typeof termDisplayAsFunc === 'function' ? termDisplayAsFunc(term) : null,
+                            'count': 0,
                             'total': termTotals[term].total,
                             'date': for_date
                         });
@@ -317,11 +319,32 @@ export const commonParsingFxn = {
 
             return currentItem;
 
-        }); // We get these in decrementing order from back-end
+        });
 
         commonParsingFxn.fillMissingChildBuckets(aggsList, Array.from(termsInAllItems));
 
-        return aggsList;
+        // remove children term if all is zero
+        const filterZeroTotalTerms = (list) => {
+            const termTotals = {};
+
+            list.forEach((item) => {
+                item.children.forEach((child) => {
+                    if (!termTotals[child.term]) {
+                        termTotals[child.term] = 0;
+                    }
+                    termTotals[child.term] += child.total;
+                });
+            });
+
+            return list.map((item) => {
+                return {
+                    ...item,
+                    children: item.children.filter((child) => termTotals[child.term] !== 0),
+                };
+            });
+        };
+
+        return filterZeroTotalTerms(aggsList);
     }
 };
 
@@ -961,6 +984,11 @@ export function UsageStatsView(props){
     const isSticky = true; //!_.any(_.values(tableToggle), (v)=> v === true);
     const commonTableProps = { windowWidth, href, session, schemas, transposed, dateRoundInterval, cumulativeSum, hideEmptyColumns, chartToggles };
 
+    let topFileLimit = 0;
+    if (countBy.file_downloads && countBy.file_downloads.indexOf('top_files') === 0) {
+        topFileLimit = 10; // parseInt(countBy.file_downloads.substring('top_files_'.length));
+    }
+
     return (
         <div className="stats-charts-container" key="charts" id="usage">
 
@@ -1029,7 +1057,8 @@ export function UsageStatsView(props){
                         <StatisticsTable data={file_downloads}
                             key={'dt_file_downloads'}
                             {...commonTableProps}
-                            containerId="content_file_downloads" />
+                            containerId="content_file_downloads"
+                            limit={topFileLimit} />
                     }
 
                     <AreaChartContainer {...commonContainerProps} id="file_downloads_volume" defaultHeight={fileDownloadsChartHeight}
@@ -1045,7 +1074,8 @@ export function UsageStatsView(props){
                             key={'dt_file_downloads_volume'}
                             valueLabel="GB"
                             {...commonTableProps}
-                            containerId="content_file_downloads_volume" />
+                            containerId="content_file_downloads_volume"
+                            limit={topFileLimit} />
                     }
 
                     <p className="fst-italic mt-2">Download tracking started in August 2018 | Re-Implemented in Feb 2020 and August 2023</p>
@@ -1510,8 +1540,8 @@ const ChartSubTitle = memoize(function ({ data, invalidDateRange }) {
  */
 const StatisticsTable = React.memo((props) => {
     const {
-        data, valueLabel = null, session, schemas, containerId = '',
-        href, dateRoundInterval,  transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
+        data, termColHeader = null, valueLabel = null, session, schemas, containerId = '',
+        href, dateRoundInterval, transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
         limit = 0, excludeNones = false, // limit and excludeNones are evaluated for only transposed data
         rowHeight = 31
     } = props;
@@ -1562,10 +1592,10 @@ const StatisticsTable = React.memo((props) => {
         // date or term column based on transposed or not
         let cols = {
             'display_title': {
-                title: transposed ? 'Term' : 'Date',
+                title: transposed ? (termColHeader || 'Term') : 'Date',
                 type: 'string',
                 noSort: true,
-                widthMap: transposed ? { 'lg': 250, 'md': 200, 'sm': 200 } : { 'lg': 200, 'md': 200, 'sm': 200 },
+                widthMap: transposed ? { 'lg': 400, 'md': 200, 'sm': 200 } : { 'lg': 200, 'md': 200, 'sm': 200 },
                 render: function (result) {
                     // overall sum
                     const overallSum = roundValue(result.overall_sum || 0, valueLabel);
@@ -1630,7 +1660,7 @@ const StatisticsTable = React.memo((props) => {
         }
 
         setColumns(cols);
-        const colDefs = _.map(_.pairs(cols), function (p) { return { field: p[0], ...p[1] } });
+        const colDefs = _.map(_.pairs(cols), function (p) { return { field: p[0], ...p[1] }; });
         setColumnDefinitions(colDefs);
 
         // create @graph
@@ -1643,7 +1673,7 @@ const StatisticsTable = React.memo((props) => {
                     return memo2;
                 }, {}),
                 '@type': ['Item'],
-                'overall_sum': !cumulativeSum ? (d.total || 0) : _.reduce(d.children, (memo, c) => memo + c.count, 0),
+                'overall_sum': !cumulativeSum ? (d.total || 0) : _.reduce(d.children, (memo, c) => memo + c.count, 0),
                 'date_created': transposed ? d.term : d.date
             };
         });
@@ -1678,7 +1708,7 @@ const StatisticsTable = React.memo((props) => {
     const modalProps = {
         ...{ dateRoundInterval, schemas },
         forDate: modalForDate,
-        onTrackingItemViewerCancel: () => setShowModal(false)
+        onHide: () => setShowModal(false)
     };
 
     return (
@@ -1696,10 +1726,10 @@ const StatisticsTable = React.memo((props) => {
 });
 
 /**
- * displays relevant tracking item (fetched via ajax call) in item detail list
+ * displays tracking item ajax-fetched in ItemDetailList
  */
 const TrackingItemViewer = React.memo(function (props) {
-    const { schemas, forDate, dateRoundInterval='day', reportName, onTrackingItemViewerCancel } = props;
+    const { schemas, forDate, dateRoundInterval='day', reportName, onHide } = props;
 
     const [isLoading, setIsLoading] = useState(true);
     const [trackingItem, setTrackingItem] = useState();
@@ -1728,7 +1758,7 @@ const TrackingItemViewer = React.memo(function (props) {
     }, [forDate, dateRoundInterval, reportName]);
 
     return (
-        <Modal show size="xl" onHide={onTrackingItemViewerCancel} className="tracking-item-viewer">
+        <Modal show size="xl" onHide={onHide} className="tracking-item-viewer">
             <Modal.Header closeButton>
                 <Modal.Title>{forDate}</Modal.Title>
             </Modal.Header>
@@ -1746,6 +1776,6 @@ const TrackingItemViewer = React.memo(function (props) {
 TrackingItemViewer.propTypes = {
     forDate: PropTypes.string.isRequired,
     dateRoundInterval: PropTypes.oneOf(['daily', 'monthly']),
-    onTrackingItemViewerCancel: PropTypes.func.isRequired,
+    onHide: PropTypes.func.isRequired,
     schemas: PropTypes.object
 };
\ No newline at end of file

From 436d3d51f20d2127822dfbd92785a12cc41dd78f Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 17:08:33 +0300
Subject: [PATCH 11/34] bug fix for fillMissingChildBuckets

---
 .../static-pages/components/StatisticsPageViewBody.js           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 38d52fa5de..d7fd9bc51b 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -99,7 +99,7 @@ export const commonParsingFxn = {
                 'date' : todayAsString,
                 'count' : 0,
                 'children' : aggsList[aggsList.length - 1].children.map(function(c){
-                    return _.extend({}, c, { 'date' : todayAsString, 'count' : 0 });
+                    return _.extend({}, c, { 'date' : todayAsString, 'count' : 0, 'total': 0 });
                 })
             });
         }

From 80a34ec8cd952c574a68367b701008d57c5aeabc Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 22:42:16 +0300
Subject: [PATCH 12/34] improve tracking item viewer style

---
 .../static/scss/encoded/modules/_charts.scss    | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/encoded/static/scss/encoded/modules/_charts.scss b/src/encoded/static/scss/encoded/modules/_charts.scss
index 82abd6fbd7..c71489bba7 100644
--- a/src/encoded/static/scss/encoded/modules/_charts.scss
+++ b/src/encoded/static/scss/encoded/modules/_charts.scss
@@ -1432,6 +1432,23 @@ $workflow-node-color-type-global-context: #ffb3b3;
 
 }
 
+body[data-path="/statistics"] {
+    .tracking-item-viewer {
+        div[data-for-field="reports"] + div.data-display {
+            .list-item {
+                .item-label, .item-value {
+                    max-width: 100% !important;
+                    flex: 0 0 100% !important;
+                }
+                .item-label {
+                    margin-top: 20px;
+                    font-size: 110%;
+                }
+            }
+        } 
+    }
+}
+
 
 /**** Cursor Component(s) ****/
 

From 4e10906b4debfb829f80f6d92f286fd95b05f593 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 22:43:13 +0300
Subject: [PATCH 13/34] show usage tab filter/settings always and hide toggles
 for submissions tab

---
 .../components/StatisticsPageViewBody.js      | 114 ++++++++++--------
 1 file changed, 66 insertions(+), 48 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index d7fd9bc51b..0f31273db1 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -932,14 +932,6 @@ export function UsageStatsView(props){
         smoothEdges, onChartToggle, onSmoothEdgeToggle, cumulativeSum, onCumulativeSumToggle
     } = props;
 
-    if (loadingStatus === 'failed'){
-        return <div className="stats-charts-container" key="charts" id="usage"><ErrorIcon/></div>;
-    }
-
-    if (!mounted || (loadingStatus === 'loading' && (!file_downloads && !sessions_by_country))){
-        return <div className="stats-charts-container" key="charts" id="usage"><LoadingIcon/></div>;
-    }
-
     const [transposed, setTransposed] = useState(true);
     const [hideEmptyColumns, setHideEmptyColumns] = useState(true);
     const [ scale, setScale ] = useState({ yAxisScale: 'Pow', yAxisPower: 0.7 });
@@ -989,44 +981,65 @@ export function UsageStatsView(props){
         topFileLimit = 10; // parseInt(countBy.file_downloads.substring('top_files_'.length));
     }
 
+    const settings = () => (
+        <GroupByDropdown {...{ groupByOptions, loadingStatus, handleGroupByChange, currentGroupBy }}
+            title="Show" outerClassName={"dropdown-container mb-0" + (isSticky ? " sticky-top" : "")}>
+            <div className="d-inline-block ms-15 me-15">
+                <Checkbox checked={smoothEdges} onChange={onSmoothEdgeToggle} data-tip="Toggle between smooth/sharp edges">Smooth Edges</Checkbox>
+            </div>
+            <div className="d-inline-block me-15">
+                <Checkbox checked={cumulativeSum} onChange={onCumulativeSumToggle} data-tip="Show as cumulative sum">Cumulative Sum</Checkbox>
+            </div>
+            <div className="d-inline-block me-15">
+                <Checkbox checked={transposed} onChange={() => setTransposed(!transposed)} data-tip="Transpose data table">Transpose Data</Checkbox>
+            </div>
+            <div className="d-inline-block me-15">
+                <Checkbox checked={hideEmptyColumns} onChange={() => setHideEmptyColumns(!hideEmptyColumns)} data-tip="Hide empty data table columns">Hide Empty Columns</Checkbox>
+            </div>
+            <div className="d-inline-block mt-06">
+                <div className="d-md-flex">
+                    <span className="text-500 me-1">Y-Axis scale:</span>
+                    <div className="me-05">
+                        <DropdownButton size="sm"
+                            title={(scale && scale['yAxisScale'] && UsageStatsView.yScaleLabels[scale['yAxisScale']]) || '-'}
+                            onSelect={(e) => setScale({ yAxisScale: e, yAxisPower: e === 'Pow' ? 0.5 : 50 })}>
+                            <DropdownItem eventKey={'Linear'} key={'scale-linear'} >{UsageStatsView.yScaleLabels['Linear']}</DropdownItem>
+                            <DropdownItem eventKey={'Pow'} key={'scale-pow'} >{UsageStatsView.yScaleLabels['Pow']}</DropdownItem>
+                            <DropdownItem eventKey={'Symlog'} key={'scale-log'} >{UsageStatsView.yScaleLabels['Symlog']}</DropdownItem>
+                        </DropdownButton>
+                    </div>
+                    <div className={"ms-md-15" + (showScaleRange ? " d-block d-md-inline-block" : " d-none")}>
+                        <input type="range" id="input_range_y_scale_power" className="w-75"
+                            min={scaleRangeMin} max={scaleRangeMax} step={scaleRangeStep} value={scale['yAxisPower']} data-tip={scaleRangeTooltip}
+                            onChange={(e) => setScale({ yAxisScale: scale['yAxisScale'], yAxisPower: e.target.valueAsNumber })} />
+                        <span className="ms-05">{scale['yAxisPower']}</span>
+                    </div>
+                </div>
+            </div>
+        </GroupByDropdown>
+    );
+
+    if (loadingStatus === 'failed'){
+        return (
+            <div className="stats-charts-container" key="charts" id="usage">
+                {settings()}
+                <ErrorIcon />
+            </div>
+        );
+    }
+
+    if (!mounted || (loadingStatus === 'loading' && (!file_downloads && !sessions_by_country))){
+        return (
+            <div className="stats-charts-container" key="charts" id="usage">
+                <LoadingIcon />
+            </div>
+        );
+    }
+
     return (
         <div className="stats-charts-container" key="charts" id="usage">
 
-            <GroupByDropdown {...{ groupByOptions, loadingStatus, handleGroupByChange, currentGroupBy }}
-                title="Show" outerClassName={"dropdown-container mb-0" + (isSticky ? " sticky-top" : "")}>
-                <div className="d-inline-block ms-15 me-15">
-                    <Checkbox checked={smoothEdges} onChange={onSmoothEdgeToggle} data-tip="Toggle between smooth/sharp edges">Smooth Edges</Checkbox>
-                </div>
-                <div className="d-inline-block me-15">
-                    <Checkbox checked={cumulativeSum} onChange={onCumulativeSumToggle} data-tip="Show as cumulative sum">Cumulative Sum</Checkbox>
-                </div>
-                <div className="d-inline-block me-15">
-                    <Checkbox checked={transposed} onChange={() => setTransposed(!transposed)} data-tip="Transpose data table">Transpose Data</Checkbox>
-                </div>
-                <div className="d-inline-block me-15">
-                    <Checkbox checked={hideEmptyColumns} onChange={() => setHideEmptyColumns(!hideEmptyColumns)} data-tip="Hide empty data table columns">Hide Empty Columns</Checkbox>
-                </div>
-                <div className="d-inline-block mt-06">
-                    <div className="d-md-flex">
-                        <span className="text-500 me-1">Y-Axis scale:</span>
-                        <div className="me-05">
-                            <DropdownButton size="sm"
-                                title={(scale && scale['yAxisScale'] && UsageStatsView.yScaleLabels[scale['yAxisScale']]) || '-'}
-                                onSelect={(e) => setScale({ yAxisScale: e, yAxisPower: e === 'Pow' ? 0.5 : 50 })}>
-                                <DropdownItem eventKey={'Linear'} key={'scale-linear'} >{UsageStatsView.yScaleLabels['Linear']}</DropdownItem>
-                                <DropdownItem eventKey={'Pow'} key={'scale-pow'} >{UsageStatsView.yScaleLabels['Pow']}</DropdownItem>
-                                <DropdownItem eventKey={'Symlog'} key={'scale-log'} >{UsageStatsView.yScaleLabels['Symlog']}</DropdownItem>
-                            </DropdownButton>
-                        </div>
-                        <div className={"ms-md-15" + (showScaleRange ? " d-block d-md-inline-block" : " d-none")}>
-                            <input type="range" id="input_range_y_scale_power" className="w-75"
-                                min={scaleRangeMin} max={scaleRangeMax} step={scaleRangeStep} value={scale['yAxisPower']} data-tip={scaleRangeTooltip}
-                                onChange={(e) => setScale({ yAxisScale: scale['yAxisScale'], yAxisPower: e.target.valueAsNumber })} />
-                            <span className="ms-05">{scale['yAxisPower']}</span>
-                        </div>
-                    </div>
-                </div>
-            </GroupByDropdown>
+            {settings()}
 
             { session && file_downloads ?
 
@@ -1345,7 +1358,8 @@ export function SubmissionsStatsView(props) {
                                 <span className="text-300">internal vs public release</span>
                             </h3>
                         }
-                        subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={expsets_released_vs_internal} />}>
+                        subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={expsets_released_vs_internal} />}
+                        hideChartButton hideTableButton>
                         <AreaChart {...commonChartProps} data={expsets_released_vs_internal} />
                     </AreaChartContainer>
 
@@ -1374,7 +1388,8 @@ export function SubmissionsStatsView(props) {
                             <span className="text-300 d-none d-sm-inline"> - </span>
                             <span className="text-300">{session ? 'publicly released' : 'released'}</span>
                         </h3>}
-                    subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={expsets_released} />}>
+                    subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={expsets_released} />}
+                    hideChartButton hideTableButton>
                     <AreaChart {...commonChartProps} data={expsets_released} />
                 </AreaChartContainer>
 
@@ -1387,7 +1402,8 @@ export function SubmissionsStatsView(props) {
                                 <span className="text-300">released (public or within 4DN)</span>
                             </h3>
                         }
-                        subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={expsets_released_internal} />}>
+                        subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={expsets_released_internal} />}
+                        hideChartButton hideTableButton>
                         <AreaChart {...commonChartProps} data={expsets_released_internal} />
                     </AreaChartContainer>
                     : null }
@@ -1400,7 +1416,8 @@ export function SubmissionsStatsView(props) {
                             <span className="text-300">{session ? 'publicly released' : 'released'}</span>
                         </h3>
                     }
-                    subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={files_released} />}>
+                    subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={files_released} />}
+                    hideChartButton hideTableButton>
                     <AreaChart {...commonChartProps} data={files_released} />
                 </AreaChartContainer>
 
@@ -1412,7 +1429,8 @@ export function SubmissionsStatsView(props) {
                             <span className="text-300">{session ? 'publicly released' : 'released'}</span>
                         </h3>
                     }
-                    subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={file_volume_released} />}>
+                    subTitle={<ChartSubTitle invalidDateRange={invalidDateRange} data={file_volume_released} />}
+                    hideChartButton hideTableButton>
                     <AreaChart {...commonChartProps} data={file_volume_released} yAxisLabel="GB" />
                 </AreaChartContainer>
 

From 4c51ba5414b7544500d990d4507d451f82bb08ae Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 30 Dec 2024 22:47:50 +0300
Subject: [PATCH 14/34] disable tracking item details viewer for anonymous
 users

---
 .../static-pages/components/StatisticsPageViewBody.js         | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 0f31273db1..555120f041 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -1656,7 +1656,7 @@ const StatisticsTable = React.memo((props) => {
                     widthMap: { 'lg': 140, 'md': 120, 'sm': 120 },
                     render: function (result) {
                         if (result[dataKey] !== 0) {
-                            return (
+                            return session ? (
                                 <a href="#"
                                     onClick={(e) => {
                                         setModalForDate(transposed ? dataKey : result.display_title);
@@ -1667,7 +1667,7 @@ const StatisticsTable = React.memo((props) => {
                                     className="value text-end fw-bold">
                                     {roundValue(result[dataKey], valueLabel)}
                                 </a>
-                            );
+                            ) : (<span className="value text-end">{roundValue(result[dataKey], valueLabel)}</span>);
                         } else {
                             return (<span className="value text-end">0</span>);
                         }

From c140deecc5a1a4e138c7b0c70addec0212322eaf Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Tue, 31 Dec 2024 00:08:41 +0300
Subject: [PATCH 15/34] decrease first column's default width

---
 .../static-pages/components/StatisticsPageViewBody.js           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 555120f041..7453fde22a 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -1613,7 +1613,7 @@ const StatisticsTable = React.memo((props) => {
                 title: transposed ? (termColHeader || 'Term') : 'Date',
                 type: 'string',
                 noSort: true,
-                widthMap: transposed ? { 'lg': 400, 'md': 200, 'sm': 200 } : { 'lg': 200, 'md': 200, 'sm': 200 },
+                widthMap: transposed ? { 'lg': 300, 'md': 200, 'sm': 200 } : { 'lg': 200, 'md': 200, 'sm': 200 },
                 render: function (result) {
                     // overall sum
                     const overallSum = roundValue(result.overall_sum || 0, valueLabel);

From e47c07ecbaa38d7ff7c0c8bcfab42277a1ca019b Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Tue, 31 Dec 2024 13:24:40 +0300
Subject: [PATCH 16/34] required webpack upgrade to fix vulnerability

---
 package-lock.json | 30 ++++++------------------------
 package.json      |  2 +-
 2 files changed, 7 insertions(+), 25 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 86345732fe..bfe2ebbb33 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -87,7 +87,7 @@
         "string-replace-loader": "^3.1.0",
         "terser-webpack-plugin": "^5.3.6",
         "utf-8-validate": "^5.0.9",
-        "webpack": "5.92.1",
+        "webpack": "5.94.0",
         "webpack-bundle-analyzer": "^4.5.0",
         "webpack-deadcode-plugin": "^0.1.15"
       },
@@ -8662,24 +8662,6 @@
       "resolved": "https://registry.npmjs.org/@types/earcut/-/earcut-2.1.4.tgz",
       "integrity": "sha512-qp3m9PPz4gULB9MhjGID7wpo3gJ4bTGXm7ltNDsmOvsPduTeHp8wSW9YckBj3mljeOh4F0m2z/0JKAALRKbmLQ=="
     },
-    "node_modules/@types/eslint": {
-      "version": "8.56.9",
-      "resolved": "https://registry.npmjs.org/@types/eslint/-/eslint-8.56.9.tgz",
-      "integrity": "sha512-W4W3KcqzjJ0sHg2vAq9vfml6OhsJ53TcUjUqfzzZf/EChUtwspszj/S0pzMxnfRcO55/iGq47dscXw71Fxc4Zg==",
-      "dependencies": {
-        "@types/estree": "*",
-        "@types/json-schema": "*"
-      }
-    },
-    "node_modules/@types/eslint-scope": {
-      "version": "3.7.7",
-      "resolved": "https://registry.npmjs.org/@types/eslint-scope/-/eslint-scope-3.7.7.tgz",
-      "integrity": "sha512-MzMFlSLBqNF2gcHWO0G1vP/YQyfvrxZ0bF+u7mzUdZ1/xK4A4sru+nraZz5i3iEIk1l1uyicaDVTB4QbbEkAYg==",
-      "dependencies": {
-        "@types/eslint": "*",
-        "@types/estree": "*"
-      }
-    },
     "node_modules/@types/estree": {
       "version": "1.0.5",
       "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.5.tgz",
@@ -35352,11 +35334,11 @@
       }
     },
     "node_modules/webpack": {
-      "version": "5.92.1",
-      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.92.1.tgz",
-      "integrity": "sha512-JECQ7IwJb+7fgUFBlrJzbyu3GEuNBcdqr1LD7IbSzwkSmIevTm8PF+wej3Oxuz/JFBUZ6O1o43zsPkwm1C4TmA==",
+      "version": "5.94.0",
+      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.94.0.tgz",
+      "integrity": "sha512-KcsGn50VT+06JH/iunZJedYGUJS5FGjow8wb9c0v5n1Om8O1g4L6LjtfxwlXIATopoQu+vOXXa7gYisWxCoPyg==",
+      "license": "MIT",
       "dependencies": {
-        "@types/eslint-scope": "^3.7.3",
         "@types/estree": "^1.0.5",
         "@webassemblyjs/ast": "^1.12.1",
         "@webassemblyjs/wasm-edit": "^1.12.1",
@@ -35365,7 +35347,7 @@
         "acorn-import-attributes": "^1.9.5",
         "browserslist": "^4.21.10",
         "chrome-trace-event": "^1.0.2",
-        "enhanced-resolve": "^5.17.0",
+        "enhanced-resolve": "^5.17.1",
         "es-module-lexer": "^1.2.1",
         "eslint-scope": "5.1.1",
         "events": "^3.2.0",
diff --git a/package.json b/package.json
index 98f6396f89..ccfe3be555 100644
--- a/package.json
+++ b/package.json
@@ -100,7 +100,7 @@
     "string-replace-loader": "^3.1.0",
     "terser-webpack-plugin": "^5.3.6",
     "utf-8-validate": "^5.0.9",
-    "webpack": "5.92.1",
+    "webpack": "5.94.0",
     "webpack-bundle-analyzer": "^4.5.0",
     "webpack-deadcode-plugin": "^0.1.15"
   },

From 5b346df3a73b14cbdad1c805c804a47113c79d05 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Tue, 31 Dec 2024 14:15:20 +0300
Subject: [PATCH 17/34] bump vitessce (3.4.14)

---
 package-lock.json | 11664 +++++++++++++++++++-------------------------
 package.json      |     2 +-
 2 files changed, 4961 insertions(+), 6705 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index bfe2ebbb33..a8a1ec67b8 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -46,7 +46,7 @@
         "underscore": "^1.13.6",
         "url": "^0.11.0",
         "uuid": "^8.3.2",
-        "vitessce": "3.4.9"
+        "vitessce": "3.4.14"
       },
       "devDependencies": {
         "@babel/core": "^7.23.7",
@@ -2035,9 +2035,10 @@
       "dev": true
     },
     "node_modules/@babel/runtime": {
-      "version": "7.25.6",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.25.6.tgz",
-      "integrity": "sha512-VBj9MYyDb9tuLq7yzqjgzt6Q+IBQLrGZfdjOekyEirZPHxXWoTSGUTMrpsfi58Up73d13NfYLv8HT9vmznjzhQ==",
+      "version": "7.26.0",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.26.0.tgz",
+      "integrity": "sha512-FDSOghenHTiToteC/QRlv2q3DhPZ/oOXTBoirfWNx1Cx3TMVcGWQtMMmQcSvb/JjpNeGzx8Pq/b4fKEJuWm1sw==",
+      "license": "MIT",
       "dependencies": {
         "regenerator-runtime": "^0.14.0"
       },
@@ -2104,6 +2105,7 @@
       "version": "0.2.1",
       "resolved": "https://registry.npmjs.org/@choojs/findup/-/findup-0.2.1.tgz",
       "integrity": "sha512-YstAqNb0MCN8PjdLCDfRsBcGVRN41f3vgLvaI0IrIcBp4AqILRSS0DeWNGkicC+f/zRIPJLc+9RURVSepwvfBw==",
+      "license": "MIT",
       "dependencies": {
         "commander": "^2.15.1"
       },
@@ -2114,7 +2116,8 @@
     "node_modules/@choojs/findup/node_modules/commander": {
       "version": "2.20.3",
       "resolved": "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz",
-      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ=="
+      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==",
+      "license": "MIT"
     },
     "node_modules/@colors/colors": {
       "version": "1.5.0",
@@ -2193,6 +2196,7 @@
       "resolved": "https://registry.npmjs.org/@danmarshall/deckgl-typings/-/deckgl-typings-3.5.0.tgz",
       "integrity": "sha512-YDwHoWxAUQdgSkxdqSp+CFUlzrnat9rEeRKucA8zE78iwUVkmOVCRjOrtVf1CjQuBRWhQbs/7/2V3N9wFc9rtw==",
       "hasInstallScript": true,
+      "license": "MIT",
       "dependencies": {
         "@types/hammerjs": "^2.0.36",
         "@types/react": "*",
@@ -2203,6 +2207,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/aggregation-layers/-/aggregation-layers-8.8.27.tgz",
       "integrity": "sha512-oGjpu+tER+EQOnTL6U2f3flWUoRNn4ouhETXc19i7zakV+8Av5jsdjy+zVY0tswCFFnHSCFd3qE/zZgOmqiTcw==",
+      "license": "MIT",
       "dependencies": {
         "@luma.gl/constants": "^8.5.16",
         "@luma.gl/shadertools": "^8.5.16",
@@ -2219,6 +2224,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/carto/-/carto-8.8.27.tgz",
       "integrity": "sha512-rwtvVLk8tXEUvSBNn8mFRLLboDeIRHDBx3kzv7skxkaa5nt8RaOcvlFA0T2H2jISvfFbVg2RTD3pquQEVXfNHQ==",
+      "license": "MIT",
       "dependencies": {
         "@loaders.gl/gis": "^3.2.10",
         "@loaders.gl/loader-utils": "^3.2.10",
@@ -2249,6 +2255,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/core/-/core-8.8.27.tgz",
       "integrity": "sha512-Gk9YrGGSoFL4TmP0v9GyOXReZMTBrUIU5+g6Ff4gnR6onBVLd+/XNd+IwdBPS85LlnT+/NOGNEG51qsVFrxReg==",
+      "license": "MIT",
       "dependencies": {
         "@loaders.gl/core": "^3.2.10",
         "@loaders.gl/images": "^3.2.10",
@@ -2269,6 +2276,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/extensions/-/extensions-8.8.27.tgz",
       "integrity": "sha512-gjLHHuwoBt9dK8/iOBEgBzAtfqVZ4l7nh0aFcft/jemlusb7iNSuCz2UUYx2lUDl9IBFzkEeo1aayJCkSiEkfw==",
+      "license": "MIT",
       "dependencies": {
         "@luma.gl/shadertools": "^8.5.16"
       },
@@ -2283,6 +2291,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/geo-layers/-/geo-layers-8.8.27.tgz",
       "integrity": "sha512-7tYe+fJAoo0W9t3rvek/+QeK90DBpUVnO7+9+dYND+Ge9Cok0c5gf9CB4WZ/Qlemmk1eOavdha9FsGejhpnx2A==",
+      "license": "MIT",
       "dependencies": {
         "@loaders.gl/3d-tiles": "^3.2.10",
         "@loaders.gl/gis": "^3.2.10",
@@ -2313,6 +2322,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/google-maps/-/google-maps-8.8.27.tgz",
       "integrity": "sha512-8PFscqGsNW7QqunmXJ//lm7iIW9PueRQ7i5oXgA/3MEnKEXzXUSoRW8YRqdiiG731cob2BqEHCfEgEDLlN5EDg==",
+      "license": "MIT",
       "peerDependencies": {
         "@deck.gl/core": "^8.0.0",
         "@luma.gl/constants": "^8.5.16",
@@ -2324,6 +2334,7 @@
       "version": "8.8.27",
       "resolved": "https://registry.npmjs.org/@deck.gl/json/-/json-8.8.27.tgz",
       "integrity": "sha512-h63e+he/uIzUKsMI0xDk51wtt2Bm56Xlhmsb+/y570izoL8z7leiNHXZ2DQWpqtYV9tu00QlyG+/cgLKDbgCTQ==",
+      "license": "MIT",
       "dependencies": {
         "d3-dsv": "^1.0.8",
         "expression-eval": "^2.0.0"
@@ -2335,12 +2346,14 @@
     "node_modules/@deck.gl/json/node_modules/commander": {
       "version": "2.20.3",
       "resolved": "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz",
-      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ=="
+      "integrity": "sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==",
+      "license": "MIT"
     },
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-      "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-2.2.1.tgz",
-      "integrity": "sha512-1JU/8q+VgFZyxwrJ+SVIOsh+KywWGpds3NTqikiKpDMZWScmAYyKIgqkO+ARvNWJfXeXR1zxz7aHF4u4CyH6vQ==",
-      "optional": true,
-      "peer": true,
-      "dependencies": {
-        "graceful-fs": "^4.1.11",
-        "micromatch": "^3.1.10",
-        "readable-stream": "^2.0.2"
-      },
-      "engines": {
-        "node": ">=0.10"
-      }
-    },
     "node_modules/web-worker": {
       "version": "1.3.0",
       "resolved": "https://registry.npmjs.org/web-worker/-/web-worker-1.3.0.tgz",
-      "integrity": "sha512-BSR9wyRsy/KOValMgd5kMyr3JzpdeoR9KVId8u5GVlTTAtNChlsE4yTxeY7zMdNSyOmoKBv8NH2qeRY9Tg+IaA=="
+      "integrity": "sha512-BSR9wyRsy/KOValMgd5kMyr3JzpdeoR9KVId8u5GVlTTAtNChlsE4yTxeY7zMdNSyOmoKBv8NH2qeRY9Tg+IaA==",
+      "license": "Apache-2.0"
     },
     "node_modules/webgl-constants": {
       "version": "1.1.1",
@@ -35323,7 +33546,8 @@
     "node_modules/webgl-sdf-generator": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/webgl-sdf-generator/-/webgl-sdf-generator-1.1.1.tgz",
-      "integrity": "sha512-9Z0JcMTFxeE+b2x1LJTdnaT8rT8aEp7MVxkNwoycNmJWwPdzoXzMh0BjJSh/AEFP+KPYZUli814h8bJZFIZ2jA=="
+      "integrity": "sha512-9Z0JcMTFxeE+b2x1LJTdnaT8rT8aEp7MVxkNwoycNmJWwPdzoXzMh0BjJSh/AEFP+KPYZUli814h8bJZFIZ2jA==",
+      "license": "MIT"
     },
     "node_modules/webidl-conversions": {
       "version": "7.0.0",
@@ -35630,6 +33854,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/which-boxed-primitive/-/which-boxed-primitive-1.0.2.tgz",
       "integrity": "sha512-bwZdv0AKLpplFY2KZRX6TvyuN7ojjr7lwkg6ml0roIy9YeuSr7JS372qlNW18UQYzgYK9ziGcerWqZOmEn9VNg==",
+      "dev": true,
       "dependencies": {
         "is-bigint": "^1.0.1",
         "is-boolean-object": "^1.1.0",
@@ -35714,13 +33939,13 @@
       "resolved": "https://registry.npmjs.org/winchan/-/winchan-0.2.2.tgz",
       "integrity": "sha512-pvN+IFAbRP74n/6mc6phNyCH8oVkzXsto4KCHPJ2AScniAnA1AmeLI03I2BzjePpaClGSI4GUMowzsD3qz5PRQ=="
     },
-    "node_modules/worker-farm": {
-      "version": "1.7.0",
-      "resolved": "https://registry.npmjs.org/worker-farm/-/worker-farm-1.7.0.tgz",
-      "integrity": "sha512-rvw3QTZc8lAxyVrqcSGVm5yP/IJ2UcB3U0graE3LCFoZ0Yn2x4EoVSqJKdB/T5M+FLcRPjz4TDacRf3OCfNUzw==",
-      "peer": true,
-      "dependencies": {
-        "errno": "~0.1.7"
+    "node_modules/wordwrapjs": {
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/wordwrapjs/-/wordwrapjs-5.1.0.tgz",
+      "integrity": "sha512-JNjcULU2e4KJwUNv6CHgI46UvDGitb6dGryHajXTDiLgg1/RiGoPSDw4kZfYnwGtEXf2ZMeIewDQgFGzkCB2Sg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12.17"
       }
     },
     "node_modules/wrap-ansi": {
@@ -35818,7 +34043,8 @@
     "node_modules/xml-utils": {
       "version": "1.10.1",
       "resolved": "https://registry.npmjs.org/xml-utils/-/xml-utils-1.10.1.tgz",
-      "integrity": "sha512-Dn6vJ1Z9v1tepSjvnCpwk5QqwIPcEFKdgnjqfYOABv1ngSofuAhtlugcUC3ehS1OHdgDWSG6C5mvj+Qm15udTQ=="
+      "integrity": "sha512-Dn6vJ1Z9v1tepSjvnCpwk5QqwIPcEFKdgnjqfYOABv1ngSofuAhtlugcUC3ehS1OHdgDWSG6C5mvj+Qm15udTQ==",
+      "license": "CC0-1.0"
     },
     "node_modules/xml2js": {
       "version": "0.6.2",
@@ -35857,6 +34083,7 @@
       "version": "4.0.2",
       "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
       "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==",
+      "license": "MIT",
       "engines": {
         "node": ">=0.4"
       }
@@ -35872,7 +34099,8 @@
     "node_modules/yallist": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz",
-      "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g=="
+      "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==",
+      "dev": true
     },
     "node_modules/yargs": {
       "version": "16.2.0",
@@ -35927,6 +34155,7 @@
       "version": "0.6.3",
       "resolved": "https://registry.npmjs.org/zarr/-/zarr-0.6.3.tgz",
       "integrity": "sha512-v7g3i/NfLEHtGtCEX8zl9b/LMY+8BY7fIYvbNX3nskAhliMCY5mA12jlc8Rbe91hSwL/4Nh2d3fUcVmnthXQkQ==",
+      "license": "Apache-2.0",
       "dependencies": {
         "numcodecs": "^0.2.2",
         "p-queue": "^7.1.0"
@@ -35939,24 +34168,27 @@
       "version": "0.2.2",
       "resolved": "https://registry.npmjs.org/numcodecs/-/numcodecs-0.2.2.tgz",
       "integrity": "sha512-Y5K8mv80yb4MgVpcElBkUeMZqeE4TrovxRit/dTZvoRl6YkB6WEjY+fiUjGCblITnt3T3fmrDg8yRWu0gOLjhQ==",
+      "license": "MIT",
       "engines": {
         "node": ">=12"
       }
     },
     "node_modules/zarrita": {
-      "version": "0.4.0-next.10",
-      "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.4.0-next.10.tgz",
-      "integrity": "sha512-S9SODuy40xuv4jSYP0AtfdItWOetKTyEGGRCO0uv7NQ+JY66Q/k4kvGxuM040sxVIIboKkjuA7V+pT3uyPtgLA==",
+      "version": "0.4.0-next.16",
+      "resolved": "https://registry.npmjs.org/zarrita/-/zarrita-0.4.0-next.16.tgz",
+      "integrity": "sha512-nCkhzMopRwDFUFDmK5RGvgvVTTf9vlElBZsrsZF97sEM3oAfv95D9VYDY7Xp489IjE6XGB8nYwsSzRO0EsUiUw==",
+      "license": "MIT",
       "dependencies": {
-        "@zarrita/core": "^0.1.0-next.8",
-        "@zarrita/indexing": "^0.1.0-next.10",
-        "@zarrita/storage": "^0.1.0-next.4"
+        "@zarrita/core": "^0.1.0-next.14",
+        "@zarrita/indexing": "^0.1.0-next.16",
+        "@zarrita/storage": "^0.1.0-next.6"
       }
     },
     "node_modules/zod": {
-      "version": "3.23.8",
-      "resolved": "https://registry.npmjs.org/zod/-/zod-3.23.8.tgz",
-      "integrity": "sha512-XBx9AXhXktjUqnepgTiE5flcKIYWi/rme0Eaj+5Y0lftuGBq+jyRu/md4WnuxqgP1ubdpNCsYEYPxrzVHD8d6g==",
+      "version": "3.24.1",
+      "resolved": "https://registry.npmjs.org/zod/-/zod-3.24.1.tgz",
+      "integrity": "sha512-muH7gBL9sI1nciMZV67X5fTKKBLtwpZ5VBp1vsOQzj1MhrBZ4wlVCm3gedKZWLp0Oyel8sIGfeiz54Su+OVT+A==",
+      "license": "MIT",
       "funding": {
         "url": "https://github.com/sponsors/colinhacks"
       }
@@ -35964,23 +34196,47 @@
     "node_modules/zstddec": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/zstddec/-/zstddec-0.1.0.tgz",
-      "integrity": "sha512-w2NTI8+3l3eeltKAdK8QpiLo/flRAr2p8AGeakfMZOXBxOg9HIu4LVDxBi81sYgVhFhdJjv1OrB5ssI8uFPoLg=="
+      "integrity": "sha512-w2NTI8+3l3eeltKAdK8QpiLo/flRAr2p8AGeakfMZOXBxOg9HIu4LVDxBi81sYgVhFhdJjv1OrB5ssI8uFPoLg==",
+      "license": "MIT AND BSD-3-Clause"
     },
     "node_modules/zustand": {
-      "version": "3.7.2",
-      "resolved": "https://registry.npmjs.org/zustand/-/zustand-3.7.2.tgz",
-      "integrity": "sha512-PIJDIZKtokhof+9+60cpockVOq05sJzHCriyvaLBmEJixseQ1a5Kdov6fWZfWOu5SK9c+FhH1jU0tntLxRJYMA==",
+      "version": "5.0.2",
+      "resolved": "https://registry.npmjs.org/zustand/-/zustand-5.0.2.tgz",
+      "integrity": "sha512-8qNdnJVJlHlrKXi50LDqqUNmUbuBjoKLrYQBnoChIbVph7vni+sY+YpvdjXG9YLd/Bxr6scMcR+rm5H3aSqPaw==",
+      "license": "MIT",
       "engines": {
-        "node": ">=12.7.0"
+        "node": ">=12.20.0"
       },
       "peerDependencies": {
-        "react": ">=16.8"
+        "@types/react": ">=18.0.0",
+        "immer": ">=9.0.6",
+        "react": ">=18.0.0",
+        "use-sync-external-store": ">=1.2.0"
       },
       "peerDependenciesMeta": {
+        "@types/react": {
+          "optional": true
+        },
+        "immer": {
+          "optional": true
+        },
         "react": {
           "optional": true
+        },
+        "use-sync-external-store": {
+          "optional": true
         }
       }
+    },
+    "node_modules/zwitch": {
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
+      "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
     }
   }
 }
diff --git a/package.json b/package.json
index ccfe3be555..e636b3f1e3 100644
--- a/package.json
+++ b/package.json
@@ -142,7 +142,7 @@
     "underscore": "^1.13.6",
     "url": "^0.11.0",
     "uuid": "^8.3.2",
-    "vitessce": "3.4.9"
+    "vitessce": "3.4.14"
   },
   "optionalDependencies": {
     "cypress": "^13.7.0"

From 1f6472a614d47b9bb2148945d6a80cae87edea4e Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Thu, 2 Jan 2025 13:19:04 +0300
Subject: [PATCH 18/34] override dependencies to use cross-spawn^7.0.5

---
 package-lock.json | 7 ++++---
 package.json      | 3 +++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index a8a1ec67b8..7edb59248b 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -16826,9 +16826,10 @@
       }
     },
     "node_modules/cross-spawn": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
-      "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==",
+      "version": "7.0.6",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
+      "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==",
+      "license": "MIT",
       "dependencies": {
         "path-key": "^3.1.0",
         "shebang-command": "^2.0.0",
diff --git a/package.json b/package.json
index e636b3f1e3..c035403b54 100644
--- a/package.json
+++ b/package.json
@@ -146,5 +146,8 @@
   },
   "optionalDependencies": {
     "cypress": "^13.7.0"
+  },
+  "overrides": {
+    "cross-spawn@<7.0.5": "^7.0.5"
   }
 }

From 27725bcf71d95e9d19041d8affe7801b1b1d46a5 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Thu, 2 Jan 2025 15:23:20 +0300
Subject: [PATCH 19/34] override dependencies to nanoid^3.3.8 (security fix)

---
 package-lock.json | 7 ++++---
 package.json      | 3 ++-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 7edb59248b..094c9541a3 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -27611,15 +27611,16 @@
       }
     },
     "node_modules/nanoid": {
-      "version": "3.3.7",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.7.tgz",
-      "integrity": "sha512-eSRppjcPIatRIMC1U6UngP8XFcz8MQWGQdt1MTBQ7NaAmvXDfvNxbvWV3x2y6CdEUciCSsDHDQZbhYaB8QEo2g==",
+      "version": "3.3.8",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.8.tgz",
+      "integrity": "sha512-WNLf5Sd8oZxOm+TzppcYk8gVOgP+l58xNy58D0nbUnOxOWRWvlcCV4kUF7ltmI6PsrLl/BgKEyS4mqsGChFN0w==",
       "funding": [
         {
           "type": "github",
           "url": "https://github.com/sponsors/ai"
         }
       ],
+      "license": "MIT",
       "bin": {
         "nanoid": "bin/nanoid.cjs"
       },
diff --git a/package.json b/package.json
index c035403b54..a4eff12bc7 100644
--- a/package.json
+++ b/package.json
@@ -148,6 +148,7 @@
     "cypress": "^13.7.0"
   },
   "overrides": {
-    "cross-spawn@<7.0.5": "^7.0.5"
+    "cross-spawn@<7.0.5": "^7.0.5",
+    "nanoid@<3.3.8": "^3.3.8"
   }
 }

From a4454e094c3b91ca53e1fb813f1ad383e770e20f Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Sun, 19 Jan 2025 00:17:52 +0300
Subject: [PATCH 20/34] bump SPC (0.1.92)

---
 package-lock.json | 4 ++--
 package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 094c9541a3..b263256671 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11,7 +11,7 @@
       "dependencies": {
         "@fortawesome/fontawesome-free": "^6.6.0",
         "@hms-dbmi-bgm/react-workflow-viz": "0.1.11",
-        "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.92b3",
+        "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.92",
         "@reduxjs/toolkit": "^2.2.6",
         "auth0-lock": "^12.5.1",
         "d3": "^7.5.0",
@@ -2670,7 +2670,7 @@
     },
     "node_modules/@hms-dbmi-bgm/shared-portal-components": {
       "version": "0.1.92",
-      "resolved": "git+ssh://git@github.com/4dn-dcic/shared-portal-components.git#465b0a84066711176b107011b3fe7c3422a326ec",
+      "resolved": "git+ssh://git@github.com/4dn-dcic/shared-portal-components.git#a35c9dc0def45dbf397e470cc9ccbc8b8b556017",
       "license": "MIT",
       "dependencies": {
         "@4dn-dcic/react-infinite": "github:4dn-dcic/react-infinite#1.1.9",
diff --git a/package.json b/package.json
index a4eff12bc7..89fc62ab63 100644
--- a/package.json
+++ b/package.json
@@ -107,7 +107,7 @@
   "dependencies": {
     "@fortawesome/fontawesome-free": "^6.6.0",
     "@hms-dbmi-bgm/react-workflow-viz": "0.1.11",
-    "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.92b3",
+    "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.92",
     "@reduxjs/toolkit": "^2.2.6",
     "auth0-lock": "^12.5.1",
     "d3": "^7.5.0",

From e2fa4d656ac0ebf7145f0eae89507ba5d2c6e245 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Sun, 19 Jan 2025 01:08:26 +0300
Subject: [PATCH 21/34] y scale refactoring

---
 .../components/StatisticsPageViewBody.js      | 142 +++++++++---------
 .../static/components/viz/AreaChart.js        |  15 +-
 .../static/scss/encoded/modules/_charts.scss  |   5 +-
 3 files changed, 87 insertions(+), 75 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 7453fde22a..6332512dc4 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -669,11 +669,13 @@ export class UsageStatsViewController extends React.PureComponent {
     static getSearchReqMomentsForTimePeriod(currentGroupBy = "daily:60") {
         let untilDate = new Date();
         let fromDate;
+        let dateIncrement = '';
 
         if (currentGroupBy.startsWith("daily:")) {
             const days = parseInt(currentGroupBy.split(":")[1], 10); // Extract the number after 'daily:'
             untilDate = sub(untilDate, { days: 1 });
             fromDate = sub(untilDate, { days }); // Go back the specified number of days
+            dateIncrement = 'daily';
         } else if (currentGroupBy.startsWith("monthly:")) {
             const [, months] = currentGroupBy.split(":");
             if (months === "All") { // Special case for 'monthly:All'
@@ -684,9 +686,10 @@ export class UsageStatsViewController extends React.PureComponent {
                 untilDate = sub(startOfMonth(untilDate), { minutes: 1 }); // Last minute of previous month
                 fromDate = sub(untilDate, { months: numMonths }); // Go back the specified number of months
             }
+            dateIncrement = 'monthly';
         }
 
-        return { fromDate, untilDate };
+        return { fromDate, untilDate, dateIncrement };
     }
 
     static defaultProps = {
@@ -779,8 +782,6 @@ export class UsageStatsViewController extends React.PureComponent {
 }
 
 
-
-
 export class SubmissionStatsViewController extends React.PureComponent {
 
     static createFileSearchUri(props, date_histogram) {
@@ -862,7 +863,6 @@ export class SubmissionStatsViewController extends React.PureComponent {
 }
 
 
-
 class UsageChartsCountByDropdown extends React.PureComponent {
 
     constructor(props){
@@ -934,47 +934,45 @@ export function UsageStatsView(props){
 
     const [transposed, setTransposed] = useState(true);
     const [hideEmptyColumns, setHideEmptyColumns] = useState(true);
-    const [ scale, setScale ] = useState({ yAxisScale: 'Pow', yAxisPower: 0.7 });
-    const { anyExpandedCharts, commonXDomain, dateRoundInterval } = useMemo(function(){
-        const { fromDate: propFromDate, untilDate: propUntilDate } = UsageStatsViewController.getSearchReqMomentsForTimePeriod(currentGroupBy);
-        let fromDate, untilDate, dateRoundInterval;
+    const [yAxisScale, setYAxisScale] = useState('Pow');
+    const [yAxisPower, setYAxisPower] = useState(0.7);
+    const handleAxisScaleChange = (scale, power) => { setYAxisScale(scale); setYAxisPower(power); };
+    const { anyExpandedCharts, commonXDomain, dateIncrement } = useMemo(function(){
+        const { fromDate: propFromDate, untilDate: propUntilDate, dateIncrement } = UsageStatsViewController.getSearchReqMomentsForTimePeriod(currentGroupBy);
+        let fromDate, untilDate;
         // We want all charts to share the same x axis. Here we round to date boundary.
         // Minor issue is that file downloads are stored in UTC/GMT while analytics are in EST timezone..
         // TODO improve on this somehow, maybe pass prop to FileDownload chart re: timezone parsing of some sort.
         if (currentGroupBy.startsWith('daily:')) {
             fromDate = add(startOfDay(propFromDate), { minutes: 15 });
             untilDate = add(endOfDay(propUntilDate), { minutes: 45 });
-            dateRoundInterval = 'day';
         } else if (currentGroupBy.startsWith('monthly:')) {
             fromDate = endOfMonth(propFromDate); // Not rly needed.
             untilDate = sub(endOfMonth(propUntilDate), { days: 1 });
-            dateRoundInterval = 'month';
-        } else if (currentGroupBy.startsWith('yearly')) { // Not yet implemented
-            dateRoundInterval = 'year';
+        } else if (currentGroupBy.startsWith('yearly')) {
+            // Not yet implemented
         }
         return {
             anyExpandedCharts: _.any(_.values(chartToggles.expanded || {})),
             commonXDomain: [fromDate, untilDate],
-            dateRoundInterval
+            dateIncrement
         };
     }, [ currentGroupBy, anyExpandedCharts ]);
 
     const commonContainerProps = { 'onToggle' : onChartToggle, chartToggles, windowWidth, 'defaultColSize' : '12', 'defaultHeight' : anyExpandedCharts ? 200 : 250 };
     const commonChartProps = {
-        dateRoundInterval,
+        dateRoundInterval: dateIncrement === 'daily' ? 'day' : (dateIncrement === 'yearly' ? 'year' : 'month'),
         'xDomain': commonXDomain,
         'curveFxn': smoothEdges ? d3.curveMonotoneX : d3.curveStepAfter,
-        cumulativeSum: cumulativeSum
+        cumulativeSum, yAxisScale, yAxisPower
     };
     const countByDropdownProps = { countBy, changeCountByForChart };
 
     const enableFileDownloadsChartTooltipItemClick = (countBy.file_downloads === 'top_files');
     const fileDownloadsChartHeight = enableFileDownloadsChartTooltipItemClick ? 350 : commonContainerProps.defaultHeight;
 
-    const { showScaleRange, scaleRangeTooltip, scaleRangeMin, scaleRangeMax, scaleRangeStep } = UsageStatsView.getYScaleDefaults(scale['yAxisScale']);
-
     const isSticky = true; //!_.any(_.values(tableToggle), (v)=> v === true);
-    const commonTableProps = { windowWidth, href, session, schemas, transposed, dateRoundInterval, cumulativeSum, hideEmptyColumns, chartToggles };
+    const commonTableProps = { windowWidth, href, session, schemas, transposed, dateIncrement, cumulativeSum, hideEmptyColumns, chartToggles };
 
     let topFileLimit = 0;
     if (countBy.file_downloads && countBy.file_downloads.indexOf('top_files') === 0) {
@@ -997,24 +995,7 @@ export function UsageStatsView(props){
                 <Checkbox checked={hideEmptyColumns} onChange={() => setHideEmptyColumns(!hideEmptyColumns)} data-tip="Hide empty data table columns">Hide Empty Columns</Checkbox>
             </div>
             <div className="d-inline-block mt-06">
-                <div className="d-md-flex">
-                    <span className="text-500 me-1">Y-Axis scale:</span>
-                    <div className="me-05">
-                        <DropdownButton size="sm"
-                            title={(scale && scale['yAxisScale'] && UsageStatsView.yScaleLabels[scale['yAxisScale']]) || '-'}
-                            onSelect={(e) => setScale({ yAxisScale: e, yAxisPower: e === 'Pow' ? 0.5 : 50 })}>
-                            <DropdownItem eventKey={'Linear'} key={'scale-linear'} >{UsageStatsView.yScaleLabels['Linear']}</DropdownItem>
-                            <DropdownItem eventKey={'Pow'} key={'scale-pow'} >{UsageStatsView.yScaleLabels['Pow']}</DropdownItem>
-                            <DropdownItem eventKey={'Symlog'} key={'scale-log'} >{UsageStatsView.yScaleLabels['Symlog']}</DropdownItem>
-                        </DropdownButton>
-                    </div>
-                    <div className={"ms-md-15" + (showScaleRange ? " d-block d-md-inline-block" : " d-none")}>
-                        <input type="range" id="input_range_y_scale_power" className="w-75"
-                            min={scaleRangeMin} max={scaleRangeMax} step={scaleRangeStep} value={scale['yAxisPower']} data-tip={scaleRangeTooltip}
-                            onChange={(e) => setScale({ yAxisScale: scale['yAxisScale'], yAxisPower: e.target.valueAsNumber })} />
-                        <span className="ms-05">{scale['yAxisPower']}</span>
-                    </div>
-                </div>
+                <AxisScale scale={yAxisScale} power={yAxisPower} onChange={handleAxisScaleChange} label="Y-Axis scale" />
             </div>
         </GroupByDropdown>
     );
@@ -1062,7 +1043,7 @@ export function UsageStatsView(props){
                         title={<h5 className="text-400 mt-0">Total File Count</h5>}
                         subTitle={enableFileDownloadsChartTooltipItemClick && <h4 className="fw-normal text-secondary">Click bar to view details</h4>}>
                         {chartToggles.chart?.file_downloads ?
-                            <AreaChart {...commonChartProps} data={file_downloads} {...scale} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} />
+                            <AreaChart {...commonChartProps} data={file_downloads} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1078,7 +1059,7 @@ export function UsageStatsView(props){
                         title={<h5 className="text-400 mt-0">Total File Size (GB)</h5>}
                         subTitle={enableFileDownloadsChartTooltipItemClick && <h4 className="fw-normal text-secondary">Click bar to view details</h4>}>
                         {chartToggles.chart?.file_downloads_volume ?
-                            <AreaChart {...commonChartProps} data={file_downloads_volume} {...scale} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} yAxisLabel="GB" />
+                            <AreaChart {...commonChartProps} data={file_downloads_volume} showTooltipOnHover={!enableFileDownloadsChartTooltipItemClick} yAxisLabel="GB" />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1113,7 +1094,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="file_views" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.file_views ?
-                            <AreaChart {...commonChartProps} data={file_views} {...scale} />
+                            <AreaChart {...commonChartProps} data={file_views} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1143,7 +1124,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="sessions_by_country" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.sessions_by_country ?
-                            <AreaChart {...commonChartProps} data={sessions_by_country} {...scale} />
+                            <AreaChart {...commonChartProps} data={sessions_by_country} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1204,7 +1185,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="experiment_set_views" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.experiment_set_views ?
-                            <AreaChart {...commonChartProps} data={experiment_set_views} {...scale} />
+                            <AreaChart {...commonChartProps} data={experiment_set_views} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1234,7 +1215,7 @@ export function UsageStatsView(props){
                         extraButtons={<UsageChartsCountByDropdown {...countByDropdownProps} chartID="fields_faceted" />}
                         legend={<HorizontalD3ScaleLegend {...{ loadingStatus }} />}>
                         {chartToggles.chart?.fields_faceted ?
-                            <AreaChart {...commonChartProps} data={fields_faceted} {...scale} />
+                            <AreaChart {...commonChartProps} data={fields_faceted} />
                             : <React.Fragment />}
                     </AreaChartContainer>
 
@@ -1279,28 +1260,6 @@ UsageStatsView.titleExtensions = {
         'sessions': 'by unique users'
     }
 };
-UsageStatsView.getYScaleDefaults = function (yScale) {
-    let showScaleRange = true;
-    let scaleRangeTooltip = '';
-    let scaleRangeMin, scaleRangeMax, scaleRangeStep;
-    //set defaults
-    if (yScale === 'Pow') {
-        scaleRangeMin = 0; scaleRangeMax = 1; scaleRangeStep = 0.1;
-        scaleRangeTooltip = 'exponent';
-    } else if (yScale === 'Symlog') {
-        scaleRangeMin = 0; scaleRangeMax = 100; scaleRangeStep = 0.5;
-        scaleRangeTooltip = 'constant';
-    } else {
-        showScaleRange = false;
-    }
-    return { showScaleRange, scaleRangeTooltip, scaleRangeMin, scaleRangeMax, scaleRangeStep };
-};
-UsageStatsView.yScaleLabels = {
-    'Linear': 'Linear',
-    'Symlog': 'Log',
-    'Pow': 'Pow'
-};
-
 
 export function SubmissionsStatsView(props) {
     const {
@@ -1559,7 +1518,7 @@ const ChartSubTitle = memoize(function ({ data, invalidDateRange }) {
 const StatisticsTable = React.memo((props) => {
     const {
         data, termColHeader = null, valueLabel = null, session, schemas, containerId = '',
-        href, dateRoundInterval, transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
+        href, dateIncrement, transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
         limit = 0, excludeNones = false, // limit and excludeNones are evaluated for only transposed data
         rowHeight = 31
     } = props;
@@ -1724,7 +1683,7 @@ const StatisticsTable = React.memo((props) => {
     };
 
     const modalProps = {
-        ...{ dateRoundInterval, schemas },
+        ...{ dateIncrement, schemas },
         forDate: modalForDate,
         onHide: () => setShowModal(false)
     };
@@ -1747,11 +1706,10 @@ const StatisticsTable = React.memo((props) => {
  * displays tracking item ajax-fetched in ItemDetailList
  */
 const TrackingItemViewer = React.memo(function (props) {
-    const { schemas, forDate, dateRoundInterval='day', reportName, onHide } = props;
+    const { schemas, forDate, dateIncrement='daily', reportName, onHide } = props;
 
     const [isLoading, setIsLoading] = useState(true);
     const [trackingItem, setTrackingItem] = useState();
-    const dateIncrement = (dateRoundInterval === 'month') ? 'monthly' : 'daily';
     const href=`/search/?type=TrackingItem&google_analytics.for_date=${forDate}&google_analytics.date_increment=${dateIncrement}`;
 
     useEffect(() => {
@@ -1793,7 +1751,53 @@ const TrackingItemViewer = React.memo(function (props) {
 });
 TrackingItemViewer.propTypes = {
     forDate: PropTypes.string.isRequired,
-    dateRoundInterval: PropTypes.oneOf(['daily', 'monthly']),
+    dateIncrement: PropTypes.oneOf(['daily', 'monthly', 'yearly']),
     onHide: PropTypes.func.isRequired,
     schemas: PropTypes.object
+};
+
+export const AxisScale = React.memo(function ({ scale, power, onChange, label = 'N/A' }) {
+    const labelPairs = _.pairs(AxisScale.labels);
+    const { showRange, rangeTooltip, rangeMin, rangeMax, rangeStep, defaultPower } = AxisScale.getDefaults(scale);
+    return (
+        <div className="d-md-flex">
+            <label className="me-1">{label}:</label>
+            <div className="mb-15">
+                <DropdownButton size="sm" title={(scale && AxisScale.labels[scale]) || '-'} onSelect={(e) => onChange(e, defaultPower)}>
+                    {
+                        labelPairs.map(([key, val]) => (
+                            <DropdownItem eventKey={key} key={key}>{val}</DropdownItem>
+                        ))
+                    }
+                </DropdownButton>
+            </div>
+            <div className={"ms-05" + (showRange ? " d-block d-md-inline-block" : " d-none")}>
+                <input type="range" id="input_range_scale_power" className="w-75"
+                    min={rangeMin} max={rangeMax} step={rangeStep} value={power} data-tip={rangeTooltip}
+                    onChange={(e) => onChange(scale, e.target.valueAsNumber)} />
+                <span className="ms-05">{power}</span>
+            </div>
+        </div>
+    );
+});
+AxisScale.labels = {
+    'Linear': 'Linear',
+    'Pow': 'Pow',
+    'Symlog': 'Log'
+};
+AxisScale.getDefaults = function (scale) {
+    let showRange = true;
+    let rangeTooltip = '';
+    let rangeMin, rangeMax, rangeStep, defaultPower;
+    //set defaults
+    if (scale === 'Pow') {
+        rangeMin = 0; rangeMax = 1; rangeStep = 0.1; defaultPower = 0.5;
+        rangeTooltip = 'exponent';
+    } else if (scale === 'Symlog') {
+        rangeMin = 0; rangeMax = 100; rangeStep = 0.5; defaultPower = 50;
+        rangeTooltip = 'constant';
+    } else {
+        showRange = false;
+    }
+    return { showRange, rangeTooltip, rangeMin, rangeMax, rangeStep, defaultPower };
 };
\ No newline at end of file
diff --git a/src/encoded/static/components/viz/AreaChart.js b/src/encoded/static/components/viz/AreaChart.js
index a1d6bc3a9c..a1e4f04648 100644
--- a/src/encoded/static/components/viz/AreaChart.js
+++ b/src/encoded/static/components/viz/AreaChart.js
@@ -483,11 +483,16 @@ export class GroupByDropdown extends React.PureComponent {
 
         return (
             <div className={outerClassName}>
-                <span className="text-500">{groupByTitle}</span>
-                <DropdownButton id={groupById} title={selectedGroupByValueTitle} onSelect={this.onGroupBySelect} style={buttonStyle} disabled={groupByOptionItems.length < 2}>
-                    {groupByOptionItems}
-                </DropdownButton>
-                {children}
+                <div className="dropdown-container-col col-12 col-lg-3 align-top">
+                    <span className="text-500 d-block mb-1">{groupByTitle}</span>
+                    <DropdownButton id={groupById} title={selectedGroupByValueTitle} onSelect={this.onGroupBySelect} style={buttonStyle} disabled={groupByOptionItems.length < 2}>
+                        {groupByOptionItems}
+                    </DropdownButton>
+                </div>
+                <div className="dropdown-container-col col-12 col-lg-9 align-top ps-1">
+                    <div className="text-500 d-block mb-1">Settings</div>
+                    {children}
+                </div>
             </div>
         );
     }
diff --git a/src/encoded/static/scss/encoded/modules/_charts.scss b/src/encoded/static/scss/encoded/modules/_charts.scss
index c71489bba7..15fcf1988a 100644
--- a/src/encoded/static/scss/encoded/modules/_charts.scss
+++ b/src/encoded/static/scss/encoded/modules/_charts.scss
@@ -1445,7 +1445,10 @@ body[data-path="/statistics"] {
                     font-size: 110%;
                 }
             }
-        } 
+        }
+        .detail-embedded-table-container {
+            max-height: none !important;
+        }
     }
 }
 

From fadce028a6b430f628fdfa220cea4d0d6ff86238 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 20 Jan 2025 23:17:01 +0300
Subject: [PATCH 22/34] decrease left margin

---
 src/encoded/static/scss/encoded/modules/_charts.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/encoded/static/scss/encoded/modules/_charts.scss b/src/encoded/static/scss/encoded/modules/_charts.scss
index 15fcf1988a..ad58a21c0f 100644
--- a/src/encoded/static/scss/encoded/modules/_charts.scss
+++ b/src/encoded/static/scss/encoded/modules/_charts.scss
@@ -1213,7 +1213,7 @@ $workflow-node-color-type-global-context: #ffb3b3;
 
             @include media-breakpoint-up(xl) {
                 .custom-date-range {
-                    margin-left: 45px;
+                    margin-left: 15px;
 
                     .form-control {
                         margin-right: 20px;

From 9d8e4ec68b7123d1cba3131f414fbe36df98068c Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 20 Jan 2025 23:18:02 +0300
Subject: [PATCH 23/34] add date interval related fields to response + update
 date range presets

---
 src/encoded/visualization.py | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/src/encoded/visualization.py b/src/encoded/visualization.py
index eaee9dccb1..c7d5cc46f2 100644
--- a/src/encoded/visualization.py
+++ b/src/encoded/visualization.py
@@ -445,6 +445,7 @@ def date_histogram_aggregations(context, request):
         'yearly'    : 'year'
     }
 
+    date_from, date_to = None, None
     try:
         json_body = request.json_body
         search_param_lists = json_body.get('search_query_params', deepcopy(DEFAULT_BROWSE_PARAM_LISTS))
@@ -477,8 +478,6 @@ def date_histogram_aggregations(context, request):
             search_param_lists = deepcopy(DEFAULT_BROWSE_PARAM_LISTS)
             del search_param_lists['award.project']
 
-
-
     if 'ExperimentSet' in search_param_lists['type'] or 'ExperimentSetReplicate' in search_param_lists['type']:
         # Add predefined sub-aggs to collect Exp and File counts from ExpSet items, in addition to getting own doc_count.
 
@@ -550,7 +549,7 @@ def date_histogram_aggregations(context, request):
                 outer_date_histogram_agg[interval + '_interval_' + dh_field]['aggs'] = histogram_sub_aggs
 
     search_param_lists['limit'] = search_param_lists['from'] = [0]
-    subreq          = make_search_subreq(request, '{}?{}'.format('/browse/', urlencode(search_param_lists, True)) )
+    subreq          = make_search_subreq(request, '{}?{}'.format('/browse/', urlencode(search_param_lists, True)))
     search_result   = perform_search_request(None, subreq, custom_aggregations=outer_date_histogram_agg)
 
     for field_to_delete in ['@context', '@id', '@type', '@graph', 'title', 'filters', 'facets', 'sort', 'clear_filters', 'actions', 'columns']:
@@ -558,19 +557,25 @@ def date_histogram_aggregations(context, request):
             continue
         del search_result[field_to_delete]
 
+    search_result['from_date'] = date_from.strftime("%Y-%m-%d") if date_from is not None else None
+    search_result['to_date'] = date_to.strftime("%Y-%m-%d") if date_to is not None else None
+    search_result['interval'] = date_histogram_intervals
+
     return search_result
 
+
 DATE_RANGE_PRESETS = {
-    'all': lambda today: (None, None),
-    'thismonth': lambda today: (today.replace(day=1), None),
+    'all': lambda today: (datetime(2017, 1, 1), today),
+    'thismonth': lambda today: (today.replace(day=1), today),
     'previousmonth': lambda today: (today.replace(day=1) - relativedelta(months=1), today.replace(day=1) - relativedelta(days=1)),
-    'last3months': lambda today: (today.replace(day=1) - relativedelta(months=2), None),
-    'last6months': lambda today: (today.replace(day=1) - relativedelta(months=5), None),
-    'last12months': lambda today: (today.replace(day=1) - relativedelta(months=11), None),
-    'thisyear': lambda today: (datetime(today.year, 1, 1), None),
+    'last3months': lambda today: (today.replace(day=1) - relativedelta(months=2), today),
+    'last6months': lambda today: (today.replace(day=1) - relativedelta(months=5), today),
+    'last12months': lambda today: (today.replace(day=1) - relativedelta(months=11), today),
+    'thisyear': lambda today: (datetime(today.year, 1, 1), datetime(today.year, 12, 31)),
     'previousyear': lambda today: (datetime(today.year - 1, 1, 1), datetime(today.year - 1, 12, 31)),
 }
 
+
 def convert_date_range(date_range_str):
     data_range_split = date_range_str.split('|')
     preset = data_range_split[0]

From 5866f5ac1172dd5ed64a1c5ec93afa9a62a94a4b Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 20 Jan 2025 23:26:12 +0300
Subject: [PATCH 24/34] add date histogram interval options

---
 .../static/components/static-pages/StatisticsPageView.js | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/encoded/static/components/static-pages/StatisticsPageView.js b/src/encoded/static/components/static-pages/StatisticsPageView.js
index 4bffbac0ff..4406fad53d 100644
--- a/src/encoded/static/components/static-pages/StatisticsPageView.js
+++ b/src/encoded/static/components/static-pages/StatisticsPageView.js
@@ -131,6 +131,13 @@ export default class StatisticsPageView extends React.PureComponent {
         };
         const initialDateRangePreset = 'all';
 
+        const dateHistogramIntervalOptions = {
+            'daily'     : <span>Daily</span>,
+            'weekly'    : <span>Weekly</span>,
+            'monthly'   : <span>Monthly</span>,
+        };
+        const initialDateHistogramInterval = 'weekly';
+
         if (browseBaseState !== 'all'){
             _.extend(groupByOptions, {
                 'award.center_title'                 : <span><i className="icon icon-fw fas icon-university me-1"/>Center</span>,
@@ -140,7 +147,7 @@ export default class StatisticsPageView extends React.PureComponent {
             initialGroupBy = 'award.center_title';
         }
         return (
-            <dynamicImports.GroupByController {...{ groupByOptions, initialGroupBy, dateRangeOptions, initialDateRangePreset }}>
+            <dynamicImports.GroupByController {...{ groupByOptions, initialGroupBy, dateRangeOptions, initialDateRangePreset, dateHistogramIntervalOptions, initialDateHistogramInterval }}>
                 <dynamicImports.SubmissionStatsViewController {..._.pick(this.props, 'session', 'browseBaseState', 'windowWidth')}>
                     <dynamicImports.StatsChartViewAggregator {...{ shouldReaggregate }} aggregationsToChartData={dynamicImports.submissionsAggsToChartData} cumulativeSum={true}>
                         <dynamicImports.SubmissionsStatsView />

From 509481864f3f859ed5f007600077f1fda4b6781c Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 20 Jan 2025 23:27:03 +0300
Subject: [PATCH 25/34] misc. date histogram interval updates for AreaChart

---
 .../static/components/viz/AreaChart.js        | 67 +++++++++++++++----
 1 file changed, 55 insertions(+), 12 deletions(-)

diff --git a/src/encoded/static/components/viz/AreaChart.js b/src/encoded/static/components/viz/AreaChart.js
index a1e4f04648..7fb3f7f438 100644
--- a/src/encoded/static/components/viz/AreaChart.js
+++ b/src/encoded/static/components/viz/AreaChart.js
@@ -280,8 +280,8 @@ export class StatsChartViewAggregator extends React.PureComponent {
 export class GroupByController extends React.PureComponent {
 
     static getDerivedStateFromProps(props, state){
-        const { groupByOptions, initialGroupBy, dateRangeOptions, initialDateRangePreset } = props;
-        const { currentGroupBy, currentDateRangePreset } = state;
+        const { groupByOptions, initialGroupBy, dateRangeOptions, initialDateRangePreset, dateHistogramIntervalOptions, initialDateHistogramInterval } = props;
+        const { currentGroupBy, currentDateRangePreset, currentDateHistogramInterval } = state;
 
         const stateObj = {};
         if (typeof groupByOptions[currentGroupBy] === 'undefined') {
@@ -300,6 +300,14 @@ export class GroupByController extends React.PureComponent {
                 _.extend(stateObj, { 'currentDateRangePreset': initialDateRangePreset });
             }
         }
+        if (dateHistogramIntervalOptions && typeof dateHistogramIntervalOptions[currentDateHistogramInterval] === 'undefined') {
+            if (typeof dateHistogramIntervalOptions[initialDateHistogramInterval] === 'undefined') {
+                logger.error('Changed props.dateHistogramIntervalOptions but state.currentDateHistogramInterval and props.initialDateHistogramInterval are now both invalid.');
+                throw new Error('Changed props.dateHistogramIntervalOptions but state.currentDateHistogramInterval and props.initialDateHistogramInterval are now both invalid.');
+            } else {
+                _.extend(stateObj, { 'currentDateHistogramInterval': initialDateHistogramInterval });
+            }
+        }
 
         return _.isEmpty(stateObj) ? null : stateObj;
     }
@@ -319,11 +327,13 @@ export class GroupByController extends React.PureComponent {
         super(props);
         this.handleGroupByChange = this.handleGroupByChange.bind(this);
         this.handleDateRangeChange = this.handleDateRangeChange.bind(this);
+        this.handleDateHistogramIntervalChange = this.handleDateHistogramIntervalChange.bind(this);
         this.state = {
             'currentGroupBy': props.initialGroupBy,
             'currentDateRangePreset': props.initialDateRangePreset,
             'currentDateRangeFrom': props.initialDateRangeFrom || null,
-            'currentDateRangeTo': props.initialDateRangeTo || null
+            'currentDateRangeTo': props.initialDateRangeTo || null,
+            'currentDateHistogramInterval': props.initialDateHistogramInterval,
         };
     }
 
@@ -351,16 +361,27 @@ export class GroupByController extends React.PureComponent {
         });
     }
 
+    handleDateHistogramIntervalChange(interval){
+        this.setState(function(currState){
+            if (currState.currentDateHistogramInterval === interval){
+                return null;
+            }
+            return { 'currentDateHistogramInterval' : interval };
+        });
+    }
+
     render(){
         const { children } = this.props;
-        const { currentGroupBy, currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo } = this.state;
+        const { currentGroupBy, currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo, currentDateHistogramInterval } = this.state;
         const childProps = _.extend(
             _.omit(this.props, 'children', 'initialGroupBy', 'initialDateRangePreset', 'initialDateRangeFrom', 'initialDateRangeTo'),
             {
                 currentGroupBy,
                 'handleGroupByChange': this.handleGroupByChange,
                 currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo,
-                'handleDateRangeChange': this.handleDateRangeChange
+                'handleDateRangeChange': this.handleDateRangeChange,
+                currentDateHistogramInterval,
+                'handleDateHistogramIntervalChange': this.handleDateHistogramIntervalChange
             });
 
         if (Array.isArray(children)){
@@ -390,6 +411,7 @@ export class GroupByDropdown extends React.PureComponent {
         super(props);
         this.onGroupBySelect = _.throttle(this.onGroupBySelect.bind(this), 1000);
         this.onDateRangeSelect = this.onDateRangeSelect.bind(this);
+        this.onDateHistogramIntervalSelect = this.onDateHistogramIntervalSelect.bind(this);
         //used as workaround to fix input type="date" unwanted reset bug
         this.state = {
             'tempDateRangeFrom': '',
@@ -426,12 +448,22 @@ export class GroupByDropdown extends React.PureComponent {
         handleDateRangeChange(presetField, from, to);
     }
 
+    onDateHistogramIntervalSelect(eventKey, evt){
+        const { handleDateHistogramIntervalChange } = this.props;
+        if (typeof handleDateHistogramIntervalChange !== 'function'){
+            throw new Error("No handleDateHistogramIntervalChange function passed to GroupByDropdown.");
+        }
+        handleDateHistogramIntervalChange(eventKey);
+    }
+
     render(){
         const {
             groupByOptions, currentGroupBy, groupByTitle,
             dateRangeOptions, currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo, dateRangeTitle,
+            dateHistogramIntervalOptions, currentDateHistogramInterval,
             loadingStatus, buttonStyle, outerClassName, children,
-            groupById, dateRangeId } = this.props;
+            groupById, dateRangeId, dateHistogramIntervalId
+        } = this.props;
         const { tempDateRangeFrom, tempDateRangeTo } = this.state;
         // group by
         const groupByOptionItems = _.map(_.pairs(groupByOptions), ([field, title]) =>
@@ -444,20 +476,24 @@ export class GroupByDropdown extends React.PureComponent {
                 <DropdownItem eventKey={field} key={field} active={field === currentDateRangePreset}>{title}</DropdownItem>
             );
             const selectedDateRangeValueTitle = (loadingStatus === 'loading' ? <i className="icon icon-fw icon-spin fas icon-circle-notch" /> : dateRangeOptions[currentDateRangePreset]);
-            const buttonStyleOverriden = buttonStyle && _.extend({}, buttonStyle, { 'marginLeft': 0 });
+            // date histogram interval
+            const dateHistogramInvervalOptionItems = _.map(_.pairs(dateHistogramIntervalOptions), ([interval, title]) =>
+                <DropdownItem eventKey={interval} key={interval} active={interval === currentDateHistogramInterval}>{title}</DropdownItem>
+            );
+            const selectedDateHistogramIntervalValueTitle = loadingStatus === 'loading' ? <i className="icon icon-fw icon-spin fas icon-circle-notch" /> : dateHistogramIntervalOptions[currentDateHistogramInterval];
             return (
                 <div className={outerClassName}>
-                    <div className="dropdown-container-col col-12 col-lg-3 align-top ps-2 pe-2">
+                    <div className="dropdown-container-col col-12 col-lg-2 align-top ps-2 pe-2">
                         <div className="text-500 d-block mb-1">{groupByTitle}</div>
-                        <DropdownButton id={groupById} title={selectedGroupByValueTitle} onSelect={this.onGroupBySelect} style={buttonStyleOverriden} disabled={groupByOptionItems.length < 2}>
+                        <DropdownButton id={groupById} title={selectedGroupByValueTitle} onSelect={this.onGroupBySelect} style={buttonStyle} disabled={groupByOptionItems.length < 2} size="sm">
                             {groupByOptionItems}
                         </DropdownButton>
                     </div>
-                    <div className="dropdown-container-col col-12 col-lg-6 align-top ps-2 pe-2">
+                    <div className="dropdown-container-col col-12 col-lg-5 align-top ps-2 pe-2">
                         <div className="text-500 d-block mb-1">{dateRangeTitle}</div>
                         <div className="date-range">
                             {/* <span className="text-300 pt-05">Presets</span> */}
-                            <DropdownButton id={dateRangeId} title={selectedDateRangeValueTitle} onSelect={(e) => this.onDateRangeSelect(e, null, null)} style={buttonStyleOverriden}>
+                            <DropdownButton id={dateRangeId} title={selectedDateRangeValueTitle} onSelect={(e) => this.onDateRangeSelect(e, null, null)} style={buttonStyle} size="sm">
                                 {dateRangeOptionItems}
                             </DropdownButton>
                             <div className="d-flex custom-date-range">
@@ -473,6 +509,13 @@ export class GroupByDropdown extends React.PureComponent {
                             </div>
                         </div>
                     </div>
+                    <div className="dropdown-container-col col-12 col-lg-2 align-top">
+                        <div className="text-500 d-block mb-1">{'Histogram Interval'}</div>
+                        <DropdownButton id={dateHistogramIntervalId} title={selectedDateHistogramIntervalValueTitle}
+                            onSelect={this.onDateHistogramIntervalSelect} style={buttonStyle} disabled={dateHistogramIntervalOptions.length < 2} size="sm">
+                            {dateHistogramInvervalOptionItems}
+                        </DropdownButton>
+                    </div>
                     <div className="dropdown-container-col col-12 col-lg-3 align-top ps-2">
                         <div className="text-500 d-block mb-1">Settings</div>
                         {children}
@@ -485,7 +528,7 @@ export class GroupByDropdown extends React.PureComponent {
             <div className={outerClassName}>
                 <div className="dropdown-container-col col-12 col-lg-3 align-top">
                     <span className="text-500 d-block mb-1">{groupByTitle}</span>
-                    <DropdownButton id={groupById} title={selectedGroupByValueTitle} onSelect={this.onGroupBySelect} style={buttonStyle} disabled={groupByOptionItems.length < 2}>
+                    <DropdownButton id={groupById} title={selectedGroupByValueTitle} onSelect={this.onGroupBySelect} style={buttonStyle} disabled={groupByOptionItems.length < 2} size="sm">
                         {groupByOptionItems}
                     </DropdownButton>
                 </div>

From 09bc89d68871f0cf5e0cf90161d82427e34830ef Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Mon, 20 Jan 2025 23:31:21 +0300
Subject: [PATCH 26/34] add missing dates + various refactoring for submisson
 and usage commonParsingFxn

---
 .../components/StatisticsPageViewBody.js      | 223 +++++++++++++-----
 1 file changed, 163 insertions(+), 60 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 6332512dc4..e951e526a0 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -112,9 +112,9 @@ export const commonParsingFxn = {
      * @param {Object.<string>} [externalTermMap] - Object which maps external terms to true (external data) or false (internal data).
      * @param {boolean} [excludeChildren=false] - If true, skips aggregating up children to increase performance very slightly.
      */
-    'bucketDocCounts' : function(intervalBuckets, groupByField, externalTermMap, excludeChildren = false){
+    'bucketDocCounts' : function(intervalBuckets, groupByField, externalTermMap, fromDate, toDate, interval, excludeChildren = false){
         const subBucketKeysToDate = new Set();
-        const aggsList = intervalBuckets.map(function(bucket, index){
+        let aggsList = intervalBuckets.map(function(bucket, index){
             const {
                 doc_count,
                 key_as_string,
@@ -154,8 +154,10 @@ export const commonParsingFxn = {
             subBucketKeysToDate.add(null);
         }
 
+        aggsList = commonParsingFxn.add_missing_dates(aggsList, fromDate, toDate, interval, 'submission');
+
         // Ensure each datum has all child terms, even if blank.
-        commonParsingFxn.fillMissingChildBuckets(aggsList, _.difference([ ...subBucketKeysToDate ], (externalTermMap && _.keys(externalTermMap)) || [] ));
+        commonParsingFxn.fillMissingChildBuckets(aggsList, [...subBucketKeysToDate]/*_.difference([ ...subBucketKeysToDate ], (externalTermMap && _.keys(externalTermMap)) || [] )*/);
 
         return aggsList;
     },
@@ -166,9 +168,9 @@ export const commonParsingFxn = {
      * @param {{ key_as_string: string, doc_count: number, group_by?: { buckets: { doc_count: number, key: string  }[] } }[]} intervalBuckets - Raw aggregation results returned from ElasticSearch
      * @param {Object.<string>} [externalTermMap] - Object which maps external terms to true (external data) or false (internal data).
      */
-    'bucketTotalFilesCounts' : function(intervalBuckets, groupByField, externalTermMap){
+    'bucketTotalFilesCounts' : function(intervalBuckets, groupByField, externalTermMap, fromDate, toDate, interval){
         const subBucketKeysToDate = new Set();
-        const aggsList = intervalBuckets.map(function(bucket, index){
+        let aggsList = intervalBuckets.map(function(bucket, index){
             const {
                 key_as_string,
                 total_files : { value: totalFiles = 0 } = {},
@@ -183,7 +185,7 @@ export const commonParsingFxn = {
                 const subBucket = _.findWhere(subBuckets, { 'key' : term });
                 const count = ((subBucket && subBucket.total_files && subBucket.total_files.value) || 0);
 
-                return { term, count };
+                return { term, count, total: count };
             });
 
             return {
@@ -193,15 +195,17 @@ export const commonParsingFxn = {
             };
         });
 
+        aggsList = commonParsingFxn.add_missing_dates(aggsList, fromDate, toDate, interval, 'submission');
+
         // Ensure each datum has all child terms, even if blank.
-        commonParsingFxn.fillMissingChildBuckets(aggsList, _.difference([ ...subBucketKeysToDate ], (externalTermMap && _.keys(externalTermMap)) || [] ));
+        commonParsingFxn.fillMissingChildBuckets(aggsList, [...subBucketKeysToDate]/*_.difference([ ...subBucketKeysToDate ], (externalTermMap && _.keys(externalTermMap)) || [] )*/);
 
         return aggsList;
     },
-    'bucketTotalFilesVolume' : function(intervalBuckets, groupByField, externalTermMap){
+    'bucketTotalFilesVolume' : function(intervalBuckets, groupByField, externalTermMap, fromDate, toDate, interval){
         const gigabyte = 1024 * 1024 * 1024;
         const subBucketKeysToDate = new Set();
-        const aggsList = intervalBuckets.map(function(bucket, index){
+        let aggsList = intervalBuckets.map(function(bucket, index){
             const {
                 key_as_string,
                 total_files_volume : { value: totalFilesVolume = 0 } = {},
@@ -227,19 +231,25 @@ export const commonParsingFxn = {
             };
         });
 
+        aggsList = commonParsingFxn.add_missing_dates(aggsList, fromDate, toDate, interval, 'submission');
+
         // Ensure each datum has all child terms, even if blank.
-        commonParsingFxn.fillMissingChildBuckets(aggsList, _.difference(Array.from(subBucketKeysToDate), (externalTermMap && _.keys(externalTermMap)) || [] ));
+        commonParsingFxn.fillMissingChildBuckets(aggsList, [...subBucketKeysToDate]/*_.difference(Array.from(subBucketKeysToDate), (externalTermMap && _.keys(externalTermMap)) || [] )*/);
 
         return aggsList;
     },
-    'analytics_to_buckets' : function(resp, reportName, termBucketField, countKey, cumulativeSum, termDisplayAsFunc = null, topCount = 0){
+    'analytics_to_buckets' : function(resp, reportName, termBucketField, countKey, cumulativeSum, currentGroupBy, termDisplayAsFunc = null, topCount = 0){
         const termsInAllItems = new Set();
 
         // De-dupe -- not particularly necessary as D3 handles this, however nice to have well-formatted data.
-        const trackingItems = _.uniq(resp['@graph'], true, function(trackingItem){
+        let trackingItems = _.uniq(resp['@graph'], true, function(trackingItem){
             return trackingItem.google_analytics.for_date;
         }).reverse(); // We get these in decrementing order from back-end
 
+        // add missing dates
+        const { fromDate, untilDate, dateIncrement } = UsageStatsViewController.getSearchReqMomentsForTimePeriod(currentGroupBy);
+        trackingItems = commonParsingFxn.add_missing_dates(trackingItems, fromDate, untilDate, dateIncrement, 'google_analytics');
+
         let totalSessionsToDate = 0;
         const termTotals = {}; // e.g. { 'USA': { count: 5, total: 5 }, 'China': { count: 2, total: 2 } }
 
@@ -345,6 +355,98 @@ export const commonParsingFxn = {
         };
 
         return filterZeroTotalTerms(aggsList);
+    },
+    'add_missing_dates': function (data, fromDate, untilDate, dateIncrement = "daily", type = "google_analytics") {
+        const forAnalytics = type === "google_analytics";
+
+        const sortedData = data; // Already sorted, skip re-sorting again
+        // // Sort the data by ascending order of date
+        // const sortedData = data.sort(
+        //     (a, b) => new Date(a.google_analytics.for_date) - new Date(b.google_analytics.for_date)
+        // );
+
+        // Collect all existing dates into a Set for quick lookup
+        const existingDates = new Set(sortedData.map((d) => forAnalytics ? d.google_analytics.for_date : d.date ));
+
+        // Utility function to add days to a date
+        const addDays = function (date, days) {
+            const newDate = new Date(date);
+            newDate.setDate(newDate.getDate() + days);
+            return newDate;
+        };
+
+        // Utility function to get the next occurrence of a specific weekday
+        const getNextWeekday = function (startDate, targetWeekday) {
+            const resultDate = new Date(startDate);
+            while (resultDate.getDay() !== targetWeekday) {
+                resultDate.setDate(resultDate.getDate() + 1);
+            }
+            return resultDate;
+        };
+
+        // Initialize the current date and the end date
+        const startDate = new Date(fromDate);
+        const endDate = new Date(untilDate);
+
+        // For weekly, align the start date to the nearest matching weekday with existing data
+        let currentDate;
+        if (dateIncrement === "weekly") {
+            // Find the day of the week for the first available data point
+            const firstExistingDate = sortedData.length > 0
+                ? new Date(forAnalytics ? sortedData[0].google_analytics.for_date : sortedData[0].date)
+                : startDate;
+            const targetWeekday = firstExistingDate.getDay();
+            currentDate = getNextWeekday(startDate, targetWeekday);
+        } else {
+            currentDate = new Date(fromDate);
+        }
+
+        // Copy the existing data to a new array
+        const completeData = [...sortedData];
+
+        // Function to choose the date increment logic
+        const incrementFunc =
+            dateIncrement === "daily"
+                ? (date) => addDays(date, 1)
+                : dateIncrement === "weekly"
+                    ? (date) => addDays(date, 7)
+                    : (date) => {
+                        const newDate = new Date(date);
+                        newDate.setMonth(newDate.getMonth() + 1);
+                        return newDate;
+                    };
+
+        while (currentDate <= endDate) {
+            const currentDateString = formatDate(currentDate, 'yyyy-MM-dd');
+
+            // If the date is missing, add a placeholder entry
+            if (!existingDates.has(currentDateString)) {
+                if (forAnalytics) {
+                    completeData.push({
+                        uuid: "uuid_for_missing_date_" + currentDateString, // Generate a unique (dummy) UUID for missing dates
+                        tracking_type: "google_analytics",
+                        google_analytics: {
+                            reports: {}, // Placeholder for missing data
+                            for_date: currentDateString,
+                            date_increment: dateIncrement
+                        }
+                    });
+                } else {
+                    completeData.push({
+                        date: currentDateString,
+                        count: 0,
+                        children: []
+                    });
+                }
+            }
+            // Move to the next increment (daily, weekly, monthly)
+            currentDate = incrementFunc(currentDate);
+        }
+
+        // Return the data sorted in descending order (newest to oldest)
+        return completeData.sort(
+            (a, b) => new Date(forAnalytics ? a.google_analytics.for_date : a.date) - new Date(forAnalytics ? b.google_analytics.for_date : b.date)
+        );
     }
 };
 
@@ -354,51 +456,50 @@ const aggregationsToChartData = {
         'requires'  : 'ExperimentSetReplicatePublic',
         'function'  : function(resp, props){
             if (!resp || !resp.aggregations) return null;
-            const { aggregations : {
-                weekly_interval_public_release : { buckets: publicBuckets = [] } = {}
-            } } = resp;
+            const { interval: [interval], from_date, to_date } = resp;
+            const agg = interval + "_interval_public_release";
+            const buckets = resp && resp.aggregations[agg] && resp.aggregations[agg].buckets;
 
-            // if (publicBuckets.length < 2) return null;
+            if (!Array.isArray(buckets)) return null;
 
-            return commonParsingFxn.countsToTotals(
-                commonParsingFxn.bucketDocCounts(publicBuckets, props.currentGroupBy, props.externalTermMap),
-                props.cumulativeSum
-            );
+            const counts = commonParsingFxn.bucketDocCounts(buckets, props.currentGroupBy, props.externalTermMap, from_date, to_date, interval);
+
+            return commonParsingFxn.countsToTotals(counts, props.cumulativeSum);
         }
     },
     'expsets_released_internal' : {
         'requires'  : 'ExperimentSetReplicateInternal',
         'function'  : function(resp, props){
             if (!resp || !resp.aggregations) return null;
-            const { aggregations : {
-                weekly_interval_project_release : { buckets: internalBuckets = [] } = {}
-            } } = resp;
+            const { interval: [interval], from_date, to_date } = resp;
+            const agg = interval + "_interval_project_release";
+            const buckets = resp && resp.aggregations[agg] && resp.aggregations[agg].buckets;
 
-            // if (internalBuckets.length < 2) return null;
+            if (!Array.isArray(buckets)) return null;
 
-            return commonParsingFxn.countsToTotals(
-                commonParsingFxn.bucketDocCounts(internalBuckets, props.currentGroupBy, props.externalTermMap),
-                props.cumulativeSum
-            );
+            const counts = commonParsingFxn.bucketDocCounts(buckets, props.currentGroupBy, props.externalTermMap, from_date, to_date, interval);
+
+            return commonParsingFxn.countsToTotals(counts, props.cumulativeSum);
         }
     },
     'expsets_released_vs_internal' : {
         'requires' : 'ExperimentSetReplicatePublicAndInternal',
         'function'  : function(resp, props){
             if (!resp || !resp.aggregations) return null;
+            const { interval: [interval], from_date, to_date } = resp;
+            const publicAgg = interval + "_interval_public_release";
+            const internalAgg = interval + "_interval_project_release";
 
-            const { aggregations : {
-                weekly_interval_project_release : { buckets: internalBuckets = [] } = {},
-                weekly_interval_public_release : { buckets: publicBuckets = [] } = {}
-            } } = resp;
+            const publicBuckets = resp && resp.aggregations[publicAgg] && resp.aggregations[publicAgg].buckets;
+            const internalBuckets = resp && resp.aggregations[internalAgg] && resp.aggregations[internalAgg].buckets;
 
-            // if (internalBuckets.length < 2) return null;
-            // if (publicBuckets.length < 2) return null;
+            if (!Array.isArray(publicBuckets)) return null;
+            if (!Array.isArray(internalBuckets)) return null;
 
             function makeDatePairFxn(bkt){ return [ bkt.date, bkt ]; }
 
-            const internalList        = commonParsingFxn.bucketDocCounts(internalBuckets, props.externalTermMap, true);
-            const publicList          = commonParsingFxn.bucketDocCounts(publicBuckets,   props.externalTermMap, true);
+            const internalList        = commonParsingFxn.bucketDocCounts(internalBuckets, props.currentGroupBy, props.externalTermMap, from_date, to_date, interval, true);
+            const publicList          = commonParsingFxn.bucketDocCounts(publicBuckets, props.currentGroupBy,   props.externalTermMap, from_date, to_date, interval, true);
             const allDates            = _.uniq(_.pluck(internalList, 'date').concat(_.pluck(publicList, 'date'))).sort(); // Used as keys to zip up the non-index-aligned lists.
             const internalKeyedByDate = _.object(internalList.map(makeDatePairFxn));
             const publicKeyedByDate   = _.object(publicList.map(makeDatePairFxn));
@@ -438,32 +539,28 @@ const aggregationsToChartData = {
         'requires'  : 'ExperimentSetReplicatePublic',
         'function'  : function(resp, props){
             if (!resp || !resp.aggregations) return null;
-            const { aggregations : {
-                weekly_interval_public_release : { buckets: publicBuckets = [] } = {}
-            } } = resp;
+            const { interval: [interval], from_date, to_date } = resp;
+            const agg = interval + "_interval_public_release";
+            const buckets = resp && resp.aggregations[agg] && resp.aggregations[agg].buckets;
+            if (!Array.isArray(buckets)) return null;
 
-            // if (publicBuckets.length < 2) return null;
+            const counts = commonParsingFxn.bucketTotalFilesCounts(buckets, props.currentGroupBy, props.externalTermMap, from_date, to_date, interval);
 
-            return commonParsingFxn.countsToTotals(
-                commonParsingFxn.bucketTotalFilesCounts(publicBuckets, props.currentGroupBy, props.externalTermMap),
-                props.cumulativeSum
-            );
+            return commonParsingFxn.countsToTotals(counts, props.cumulativeSum);
         }
     },
     'file_volume_released' : {
         'requires'  : 'ExperimentSetReplicatePublic',
         'function'  : function(resp, props){
             if (!resp || !resp.aggregations) return null;
-            const { aggregations : {
-                weekly_interval_public_release : { buckets: publicBuckets = [] } = {}
-            } } = resp;
+            const { interval: [interval], from_date, to_date } = resp;
+            const agg = interval + "_interval_public_release";
+            const buckets = resp && resp.aggregations[agg] && resp.aggregations[agg].buckets;
+            if (!Array.isArray(buckets)) return null;
 
-            // if (publicBuckets.length < 2) return null;
+            const volumes = commonParsingFxn.bucketTotalFilesVolume(buckets, props.currentGroupBy, props.externalTermMap, from_date, to_date, interval);
 
-            return commonParsingFxn.countsToTotals(
-                commonParsingFxn.bucketTotalFilesVolume(publicBuckets, props.currentGroupBy, props.externalTermMap),
-                props.cumulativeSum
-            );
+            return commonParsingFxn.countsToTotals(volumes, props.cumulativeSum);
         }
     },
     'fields_faceted' : {
@@ -478,7 +575,7 @@ const aggregationsToChartData = {
             if (props.fields_faceted_group_by === 'term') groupingKey = 'ga:dimension4';
             if (props.fields_faceted_group_by === 'field+term') groupingKey = 'ga:eventLabel';
 
-            return commonParsingFxn.analytics_to_buckets(resp, 'fields_faceted', groupingKey, countKey, props.cumulativeSum);
+            return commonParsingFxn.analytics_to_buckets(resp, 'fields_faceted', groupingKey, countKey, props.cumulativeSum, props.currentGroupBy);
         }
     },
     'sessions_by_country' : {
@@ -496,7 +593,7 @@ const aggregationsToChartData = {
                 countKey = (props.countBy.sessions_by_country === 'sessions') ? 'ga:sessions' : 'ga:pageviews';
             }
 
-            return commonParsingFxn.analytics_to_buckets(resp, useReport, termBucketField, countKey, props.cumulativeSum);
+            return commonParsingFxn.analytics_to_buckets(resp, useReport, termBucketField, countKey, props.cumulativeSum, props.currentGroupBy);
         }
     },
     /*
@@ -535,7 +632,7 @@ const aggregationsToChartData = {
             if (props.countBy.experiment_set_views === 'expset_list_views') countKey = 'ga:productListViews';
             else if (props.countBy.experiment_set_views === 'expset_clicks') countKey = 'ga:productListClicks';
 
-            return commonParsingFxn.analytics_to_buckets(resp, 'views_by_experiment_set', termBucketField, countKey, props.cumulativeSum);
+            return commonParsingFxn.analytics_to_buckets(resp, 'views_by_experiment_set', termBucketField, countKey, props.cumulativeSum, props.currentGroupBy);
         }
     },
     /**
@@ -570,7 +667,7 @@ const aggregationsToChartData = {
             //if (props.file_downloads_by_experiment_type_group_by === 'term') groupingKey = 'ga:dimension4';
             //if (props.file_downloads_by_experiment_type_group_by === 'field+term') groupingKey = 'ga:eventLabel';
 
-            return commonParsingFxn.analytics_to_buckets(resp, useReport, groupingKey, countKey, props.cumulativeSum, topCount);
+            return commonParsingFxn.analytics_to_buckets(resp, useReport, groupingKey, countKey, props.cumulativeSum, props.currentGroupBy, topCount);
 
             // if (!resp || !resp.aggregations || !props.countBy || !props.countBy.file_downloads) return null;
             // const dateAggBucket = props.currentGroupBy && (props.currentGroupBy + '_interval_date_created');
@@ -611,7 +708,7 @@ const aggregationsToChartData = {
 
             //convert volume to GB
             const gigabyte = 1024 * 1024 * 1024;
-            const result = commonParsingFxn.analytics_to_buckets(resp, useReport, groupingKey, countKey, props.cumulativeSum, topCount);
+            const result = commonParsingFxn.analytics_to_buckets(resp, useReport, groupingKey, countKey, props.cumulativeSum, props.currentGroupBy, topCount);
             if (result && Array.isArray(result) && result.length > 0) {
                 _.forEach(result, (r) => {
                     r.total = r.total / gigabyte;
@@ -646,7 +743,7 @@ const aggregationsToChartData = {
                 else if (countBy === 'file_clicks') countKey = 'ga:productListClicks';
             }
 
-            return commonParsingFxn.analytics_to_buckets(resp, useReport, termBucketField, countKey, props.cumulativeSum);
+            return commonParsingFxn.analytics_to_buckets(resp, useReport, termBucketField, countKey, props.cumulativeSum, props.currentGroupBy);
         }
     },
 };
@@ -793,6 +890,9 @@ export class SubmissionStatsViewController extends React.PureComponent {
             else
                 params.date_range = `custom|${props.currentDateRangeFrom || ''}|${props.currentDateRangeTo || ''}`;
         }
+        if (props.currentDateHistogramInterval) {
+            params.date_histogram_interval = props.currentDateHistogramInterval;
+        }
         if (date_histogram) {
             params.date_histogram = Array.isArray(date_histogram) ? date_histogram : [date_histogram];
         }
@@ -820,7 +920,8 @@ export class SubmissionStatsViewController extends React.PureComponent {
                 pastProps.currentGroupBy !== nextProps.currentGroupBy ||
                 pastProps.currentDateRangePreset !== nextProps.currentDateRangePreset ||
                 pastProps.currentDateRangeFrom !== nextProps.currentDateRangeFrom ||
-                pastProps.currentDateRangeTo !== nextProps.currentDateRangeTo
+                pastProps.currentDateRangeTo !== nextProps.currentDateRangeTo ||
+                pastProps.currentDateHistogramInterval !== nextProps.currentDateHistogramInterval
             );
         }
     };
@@ -1265,6 +1366,7 @@ export function SubmissionsStatsView(props) {
     const {
         loadingStatus, mounted, session, currentGroupBy, groupByOptions, handleGroupByChange, windowWidth,
         currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo, dateRangeOptions, handleDateRangeChange,
+        currentDateHistogramInterval, dateHistogramIntervalOptions, handleDateHistogramIntervalChange,
         // Passed in from StatsChartViewAggregator:
         expsets_released, expsets_released_internal, files_released, file_volume_released,
         expsets_released_vs_internal, chartToggles, smoothEdges, width, onChartToggle, onSmoothEdgeToggle,
@@ -1289,7 +1391,8 @@ export function SubmissionsStatsView(props) {
     const commonChartProps = { 'curveFxn' : smoothEdges ? d3.curveMonotoneX : d3.curveStepAfter, cumulativeSum: cumulativeSum, xDomain };
     const groupByProps = {
         currentGroupBy, groupByOptions, handleGroupByChange,
-        currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo, dateRangeOptions, handleDateRangeChange, loadingStatus
+        currentDateRangePreset, currentDateRangeFrom, currentDateRangeTo, dateRangeOptions, handleDateRangeChange, loadingStatus,
+        currentDateHistogramInterval, dateHistogramIntervalOptions, handleDateHistogramIntervalChange,
     };
     const invalidDateRange = currentDateRangeFrom && currentDateRangeTo && currentDateRangeFrom > currentDateRangeTo;
 

From 748987b333648a395ac2aac8202b86709fc742ec Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Tue, 21 Jan 2025 00:19:08 +0300
Subject: [PATCH 27/34] disable modal for non-admins

---
 .../components/StatisticsPageViewBody.js      | 35 +++++++++++++++----
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index e951e526a0..4661c02639 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -12,7 +12,7 @@ import DropdownButton from 'react-bootstrap/esm/DropdownButton';
 import Modal from 'react-bootstrap/esm/Modal';
 
 import { Checkbox } from '@hms-dbmi-bgm/shared-portal-components/es/components/forms/components/Checkbox';
-import { console, ajax, analytics, logger } from '@hms-dbmi-bgm/shared-portal-components/es/components/util';
+import { console, ajax, JWT, analytics, logger } from '@hms-dbmi-bgm/shared-portal-components/es/components/util';
 import { navigate } from './../../util';
 import { Term } from './../../util/Schemas';
 import { ColumnCombiner, CustomColumnController, SortController } from '@hms-dbmi-bgm/shared-portal-components/es/components/browse/EmbeddedSearchView';
@@ -1072,8 +1072,14 @@ export function UsageStatsView(props){
     const enableFileDownloadsChartTooltipItemClick = (countBy.file_downloads === 'top_files');
     const fileDownloadsChartHeight = enableFileDownloadsChartTooltipItemClick ? 350 : commonContainerProps.defaultHeight;
 
+    let enableDetail = false;
+    const userGroups = (session && JWT.getUserGroups()) || null;
+    if (userGroups && userGroups.indexOf('admin') !== -1) {
+        enableDetail = true
+    }
+
     const isSticky = true; //!_.any(_.values(tableToggle), (v)=> v === true);
-    const commonTableProps = { windowWidth, href, session, schemas, transposed, dateIncrement, cumulativeSum, hideEmptyColumns, chartToggles };
+    const commonTableProps = { windowWidth, href, session, schemas, transposed, dateIncrement, cumulativeSum, hideEmptyColumns, chartToggles, enableDetail };
 
     let topFileLimit = 0;
     if (countBy.file_downloads && countBy.file_downloads.indexOf('top_files') === 0) {
@@ -1620,9 +1626,9 @@ const ChartSubTitle = memoize(function ({ data, invalidDateRange }) {
  */
 const StatisticsTable = React.memo((props) => {
     const {
-        data, termColHeader = null, valueLabel = null, session, schemas, containerId = '',
+        data, termColHeader = null, valueLabel = null, schemas, containerId = '',
         href, dateIncrement, transposed = false, windowWidth, cumulativeSum, hideEmptyColumns,
-        limit = 0, excludeNones = false, // limit and excludeNones are evaluated for only transposed data
+        session, enableDetail = false, limit = 0, excludeNones = false, // limit and excludeNones are evaluated for only transposed data
         rowHeight = 31
     } = props;
     const [columns, setColumns] = useState({});
@@ -1681,7 +1687,7 @@ const StatisticsTable = React.memo((props) => {
                     const overallSum = roundValue(result.overall_sum || 0, valueLabel);
                     const tooltip = `${result.display_title} (${overallSum})`;
 
-                    return transposed ? (
+                    return transposed || !enableDetail  ? (
                         <span className="value text-truncate text-start" data-tip={tooltip.length > 40 ? tooltip : null}>
                             {result.display_title} <strong>({overallSum})</strong>
                         </span>
@@ -1718,7 +1724,7 @@ const StatisticsTable = React.memo((props) => {
                     widthMap: { 'lg': 140, 'md': 120, 'sm': 120 },
                     render: function (result) {
                         if (result[dataKey] !== 0) {
-                            return session ? (
+                            return enableDetail ? (
                                 <a href="#"
                                     onClick={(e) => {
                                         setModalForDate(transposed ? dataKey : result.display_title);
@@ -1804,6 +1810,23 @@ const StatisticsTable = React.memo((props) => {
         </React.Fragment>
     );
 });
+StatisticsTable.propTypes = {
+    data: PropTypes.array.isRequired,
+    termColHeader: PropTypes.string,
+    valueLabel: PropTypes.string,
+    schemas: PropTypes.object,
+    containerId: PropTypes.string,
+    href: PropTypes.string,
+    dateIncrement: PropTypes.oneOf(['daily', 'monthly', 'yearly']),
+    transposed: PropTypes.bool,
+    cumulativeSum: PropTypes.bool,
+    hideEmptyColumns: PropTypes.bool,
+    session: PropTypes.object,
+    enableDetail: PropTypes.bool,
+    limit: PropTypes.number,
+    excludeNones: PropTypes.bool,
+    windowWidth: PropTypes.number
+};
 
 /**
  * displays tracking item ajax-fetched in ItemDetailList

From a875748b78d6ac4befc2e3f51c97b1651e42acd9 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Tue, 21 Jan 2025 00:20:11 +0300
Subject: [PATCH 28/34] change title background color

---
 src/encoded/static/scss/encoded/modules/_charts.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/encoded/static/scss/encoded/modules/_charts.scss b/src/encoded/static/scss/encoded/modules/_charts.scss
index ad58a21c0f..dc5dc0884e 100644
--- a/src/encoded/static/scss/encoded/modules/_charts.scss
+++ b/src/encoded/static/scss/encoded/modules/_charts.scss
@@ -1369,7 +1369,7 @@ $workflow-node-color-type-global-context: #ffb3b3;
         margin-bottom: 20px;
         padding: 10px 10px;
         border-bottom: 2px solid #f4f4f4;
-        background-color: #F1F9FF;
+        background-color: #eff7f8;
     }
     &#submissions {
         .date-range .dropdown button {

From 7d3cb7810a9deeaf74c40a2cadfb7e578cdd53c4 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Tue, 21 Jan 2025 13:33:44 +0300
Subject: [PATCH 29/34] update changelog

---
 CHANGELOG.rst | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 343ffb79b0..f410f6a506 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -6,6 +6,19 @@ fourfront
 Change Log
 ----------
 
+8.5.0
+=====
+
+`PR 1920: npm security updates + statistics page improvements <https://github.com/4dn-dcic/fourfront/pull/1920>`_
+
+* Critical npm package updates for security vulnerabilities
+* New usage statistics table shows daily counts in tabular form
+* New TrackingItem viewer triggered by usage statistics table cell click (admin-only)
+* New Y-Axis scaling for usage statistics
+* Enhanced table-full-size toggles for usage statistics
+* New histogram interval options for submission statistics
+* Chart section header styles updated
+
 
 8.4.6
 =====

From d09e25da50f892959f791b551636cd8187acae2d Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Wed, 22 Jan 2025 00:10:38 +0300
Subject: [PATCH 30/34] rename prop

---
 .../static-pages/components/StatisticsPageViewBody.js           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index 4661c02639..dd256ed836 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -1088,7 +1088,7 @@ export function UsageStatsView(props){
 
     const settings = () => (
         <GroupByDropdown {...{ groupByOptions, loadingStatus, handleGroupByChange, currentGroupBy }}
-            title="Show" outerClassName={"dropdown-container mb-0" + (isSticky ? " sticky-top" : "")}>
+            groupByTitle="Show" outerClassName={"dropdown-container mb-0" + (isSticky ? " sticky-top" : "")}>
             <div className="d-inline-block ms-15 me-15">
                 <Checkbox checked={smoothEdges} onChange={onSmoothEdgeToggle} data-tip="Toggle between smooth/sharp edges">Smooth Edges</Checkbox>
             </div>

From 7555c6f8e48396d90589c833591624401909fd89 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Wed, 22 Jan 2025 11:18:57 +0300
Subject: [PATCH 31/34] set QC report url as default hidden

---
 .../components/browse/components/file-tables.js  | 16 ++++++++++++----
 .../components/item-pages/QualityMetricView.js   |  7 +++++--
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/src/encoded/static/components/browse/components/file-tables.js b/src/encoded/static/components/browse/components/file-tables.js
index ff5bdd313c..3661201933 100644
--- a/src/encoded/static/components/browse/components/file-tables.js
+++ b/src/encoded/static/components/browse/components/file-tables.js
@@ -1097,8 +1097,13 @@ export class QCMetricsTable extends React.PureComponent {
             </React.Fragment>
         );
     }
-
-    static generateAlignedColumnHeaders(fileGroups) {
+    /**
+     * Generates column headers for QCMetricsTable including render functions for each column
+     * @param {*} fileGroups file groups
+     * @param {*} canShowMetricURL 2025-01-22: added to hide QC HTML Report Links after removal of bulk html reports already generated
+     * @returns columnHeaders for QCMetricsTable including render functions for each column
+     */
+    static generateAlignedColumnHeaders(fileGroups, canShowMetricURL = false) {
         return fileGroups.map(function (fileGroup) {
             const titleTooltipsByQMSTitle = QCMetricsTable.qcSummaryItemTitleTooltipsByTitle(fileGroup);
             const columnHeaders = [ // Static / present-for-each-table headers
@@ -1125,7 +1130,7 @@ export class QCMetricsTable extends React.PureComponent {
                 return f && f.quality_metric && f.quality_metric.url;
             });
 
-            if (anyFilesWithMetricURL) {
+            if (anyFilesWithMetricURL && canShowMetricURL) {
                 columnHeaders.push({ columnClass: 'file-detail', title: 'Report', initialWidth: 35, render: renderFileQCReportLinkButton });
                 columnHeaders.push({ columnClass: 'file-detail', title: 'Details', initialWidth: 35, render: renderFileQCDetailLinkButton });
             } else {
@@ -1235,9 +1240,12 @@ export class QCMetricsTable extends React.PureComponent {
 }
 
 export function QCMetricFromSummary(props){
-    const { title } = props;
+    const { title, field } = props;
     const { value, tooltip } = QCMetricFromSummary.formatByNumberType(props);
 
+    // 2025-01-22: added to hide QC HTML Report Links after removal of bulk html reports already generated
+    if (field === 'url') { return null; }
+
     return (
         <div className="overview-list-element">
             <div className="row">
diff --git a/src/encoded/static/components/item-pages/QualityMetricView.js b/src/encoded/static/components/item-pages/QualityMetricView.js
index 44f057d4fe..eb671a70a7 100644
--- a/src/encoded/static/components/item-pages/QualityMetricView.js
+++ b/src/encoded/static/components/item-pages/QualityMetricView.js
@@ -90,7 +90,7 @@ class QualityMetricViewOverview extends React.PureComponent {
                 <div className="overview-list-elements-container">
                     {_.map(quality_metric_summary, function (qmsItem) { return <QCMetricFromSummary {...qmsItem} key={qmsItem.title} />; })}
                     {context.url ?
-                        <QCMetricFromSummary title="Report" tooltip="Link to full quality metric report" value={
+                        <QCMetricFromSummary title="Report" tooltip="Link to full quality metric report" field="url" value={
                             <React.Fragment>
                                 <a href={context.url} target="_blank" rel="noopener noreferrer">{valueTransforms.hrefToFilename(context.url)}</a>
                                 <i className="ms-05 icon icon-fw icon-external-link-alt text-small fas" />
@@ -191,6 +191,9 @@ class QCMetricFromEmbed extends React.PureComponent {
         const { metric, qcProperty, schemaItem, schemas, fallbackTitle, tips, percent } = this.props;
         const { open, closing } = this.state;
 
+        // 2025-01-22: added to hide QC HTML Report Links after removal of bulk html reports already generated
+        if (qcProperty === "url") return null;
+
         const { qc_order = null, title = null, description: tip = null } = schemaItem || {};
         if (schemaItem && typeof qc_order !== 'number') return null;
         let value = metric[qcProperty];
@@ -326,7 +329,7 @@ export class QualityControlResults extends React.PureComponent {
             <div className="overview-list-elements-container">
                 { _.map(file.quality_metric.quality_metric_summary, function(qmsItem){ return <QCMetricFromSummary {...qmsItem} key={qmsItem.title} />; }) }
                 { metricURL ?
-                    <QCMetricFromSummary title="Report" tooltip="Link to full quality metric report" value={
+                    <QCMetricFromSummary title="Report" tooltip="Link to full quality metric report" field="url" value={
                         <React.Fragment>
                             <a href={metricURL} target="_blank" rel="noopener noreferrer">{ valueTransforms.hrefToFilename(metricURL) }</a>
                             <i className="ms-05 icon icon-fw icon-external-link-alt text-small fas"/>

From a2c0bf57f42d0fa2b8e43724ad347df6d038f9d4 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Wed, 22 Jan 2025 11:19:54 +0300
Subject: [PATCH 32/34] update changelog

---
 CHANGELOG.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f410f6a506..450ab2e752 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -18,6 +18,7 @@ Change Log
 * Enhanced table-full-size toggles for usage statistics
 * New histogram interval options for submission statistics
 * Chart section header styles updated
+* Hide QC HTML Report Links after removal of bulk html reports already generated
 
 
 8.4.6

From 0b9498ae2f79d9347043f27e4d8bd33b31f36051 Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Fri, 24 Jan 2025 10:47:56 +0300
Subject: [PATCH 33/34] horizontally center y-axis scale controls

---
 .../components/StatisticsPageViewBody.js      | 34 ++++++++++---------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
index dd256ed836..82b11a85b8 100644
--- a/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
+++ b/src/encoded/static/components/static-pages/components/StatisticsPageViewBody.js
@@ -1886,22 +1886,24 @@ export const AxisScale = React.memo(function ({ scale, power, onChange, label =
     const labelPairs = _.pairs(AxisScale.labels);
     const { showRange, rangeTooltip, rangeMin, rangeMax, rangeStep, defaultPower } = AxisScale.getDefaults(scale);
     return (
-        <div className="d-md-flex">
-            <label className="me-1">{label}:</label>
-            <div className="mb-15">
-                <DropdownButton size="sm" title={(scale && AxisScale.labels[scale]) || '-'} onSelect={(e) => onChange(e, defaultPower)}>
-                    {
-                        labelPairs.map(([key, val]) => (
-                            <DropdownItem eventKey={key} key={key}>{val}</DropdownItem>
-                        ))
-                    }
-                </DropdownButton>
-            </div>
-            <div className={"ms-05" + (showRange ? " d-block d-md-inline-block" : " d-none")}>
-                <input type="range" id="input_range_scale_power" className="w-75"
-                    min={rangeMin} max={rangeMax} step={rangeStep} value={power} data-tip={rangeTooltip}
-                    onChange={(e) => onChange(scale, e.target.valueAsNumber)} />
-                <span className="ms-05">{power}</span>
+        <div className="d-flex justify-content-center align-items-center">
+            <div className="d-md-flex align-items-center w-100">
+                <label className="me-1">{label}:</label>
+                <div>
+                    <DropdownButton size="sm" title={(scale && AxisScale.labels[scale]) || '-'} onSelect={(e) => onChange(e, defaultPower)}>
+                        {
+                            labelPairs.map(([key, val]) => (
+                                <DropdownItem eventKey={key} key={key}>{val}</DropdownItem>
+                            ))
+                        }
+                    </DropdownButton>
+                </div>
+                <div className={"ms-05" + (showRange ? " d-block d-md-inline-block" : " d-none")}>
+                    <input type="range" id="input_range_scale_power" className="w-75"
+                        min={rangeMin} max={rangeMax} step={rangeStep} value={power} data-tip={rangeTooltip}
+                        onChange={(e) => onChange(scale, e.target.valueAsNumber)} />
+                    <span className="ms-05">{power}</span>
+                </div>
             </div>
         </div>
     );

From c71a3284309e28fca50f7d352e0d4beef3109d0f Mon Sep 17 00:00:00 2001
From: utku-ozturk <utku.ozturk@karyasmd.com>
Date: Fri, 24 Jan 2025 10:48:24 +0300
Subject: [PATCH 34/34] adjust cols

---
 src/encoded/static/components/viz/AreaChart.js      | 13 +++++++------
 .../static/scss/encoded/modules/_charts.scss        |  4 ++++
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/encoded/static/components/viz/AreaChart.js b/src/encoded/static/components/viz/AreaChart.js
index 7fb3f7f438..965629133f 100644
--- a/src/encoded/static/components/viz/AreaChart.js
+++ b/src/encoded/static/components/viz/AreaChart.js
@@ -399,12 +399,13 @@ export class GroupByDropdown extends React.PureComponent {
         'groupByTitle' : "Group By",
         'dateRangeTitle' : "Date",
         'buttonStyle' : {
-            'marginLeft' : 12,
+            'marginLeft' : 0,
             'textAlign' : 'left'
         },
         'outerClassName' : "dropdown-container mb-15",
-        'groupById' : "select_primary_charts_group_by",
-        'dateRangeId' : "select_primary_charts_date_range"
+        'groupById' : "select_charts_group_by",
+        'dateRangeId' : "select_charts_date_range",
+        "dateHistogramIntervalId" : "select_charts_date_histogram_interval"
     };
 
     constructor(props){
@@ -489,7 +490,7 @@ export class GroupByDropdown extends React.PureComponent {
                             {groupByOptionItems}
                         </DropdownButton>
                     </div>
-                    <div className="dropdown-container-col col-12 col-lg-5 align-top ps-2 pe-2">
+                    <div className="dropdown-container-col col-12 col-lg-6 align-top ps-2 pe-2">
                         <div className="text-500 d-block mb-1">{dateRangeTitle}</div>
                         <div className="date-range">
                             {/* <span className="text-300 pt-05">Presets</span> */}
@@ -516,7 +517,7 @@ export class GroupByDropdown extends React.PureComponent {
                             {dateHistogramInvervalOptionItems}
                         </DropdownButton>
                     </div>
-                    <div className="dropdown-container-col col-12 col-lg-3 align-top ps-2">
+                    <div className="dropdown-container-col col-12 col-lg-2 align-top ps-2">
                         <div className="text-500 d-block mb-1">Settings</div>
                         {children}
                     </div>
@@ -1410,7 +1411,7 @@ export class AreaChartContainer extends React.Component {
             const className = "btn btn-sm me-05 " + (toggled ? "btn-primary" : "btn-outline-dark");
             buttons.push(
                 <button type="button" className={className} onClick={(e) => this.toggleButton(e, 'expanded')} data-tip="Toggle full width" key={id + '_expanded'}>
-                    <i className="icon icon-fw fas icon-search-plus" />
+                    <i className="icon icon-fw fas icon-expand-alt" />
                 </button>
             );
         }
diff --git a/src/encoded/static/scss/encoded/modules/_charts.scss b/src/encoded/static/scss/encoded/modules/_charts.scss
index dc5dc0884e..08836fbd12 100644
--- a/src/encoded/static/scss/encoded/modules/_charts.scss
+++ b/src/encoded/static/scss/encoded/modules/_charts.scss
@@ -1177,6 +1177,10 @@ $workflow-node-color-type-global-context: #ffb3b3;
             }
         }
 
+        #select_charts_date_histogram_interval {
+            min-width: 60%
+        }
+
         // .btn-primary {
         //     border: 1px solid #0B62BA;
         // }