cellbrowser 1.2.20__tar.gz → 1.2.22__tar.gz

{cellbrowser-1.2.20/src/cbPyLib/cellbrowser.egg-info → cellbrowser-1.2.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellbrowser
-Version: 1.2.20
+Version: 1.2.22
 Summary: UCSC Cellbrowser, an interactive browser for single cell data. Includes converters and basic pipelines for text files, Seurat, Scanpy and Cellranger.
 Home-page: https://github.com/maximilianh/cellBrowser
 Author: Maximilian Haeussler

{cellbrowser-1.2.20 → cellbrowser-1.2.22}/src/cbPyLib/cellbrowser/R/cellbrowser.R

@@ -386,7 +386,14 @@ ExportToCellbrowser <- function(
         #}
     #}
   if (is.null(x = cluster.field)) {
-        message("No cluster field specified: Using the value of Idents()")
+        # Do not stop here: loading the object is often the slowest step. Export everything
+        # that does not need a cluster field, skip the markers, and leave the cluster lines in
+        # cellbrowser.conf commented out with the possible fields listed, for the user to fill in.
+        warning("No cluster field was given (cluster.field='xxx' from R or -c xxx with cbImportSeurat). ",
+            "Exporting everything else, but no cluster markers will be computed. Possible meta annotation fields are: ",
+            toString(colnames(x = meta)), immediate. = TRUE)
+        if (is.null(markers.file))
+            skip.markers <- TRUE
         # create a new meta data field named "Cluster"
         #newDf <- cbind(object@meta.data, Idents(object))
         # default name is "Idents(object)", not good, let's rename that to "Cluster"
@@ -400,10 +407,6 @@ ExportToCellbrowser <- function(
       #Idents(object) <- as.factor([object[[cluster.field]], cluster.field])
   }
 
-  # make sure that we have a cluster field
-  #if (is.null(x = cluster.field))
-      #stop("There was no cluster field provided and the auto-detection to find one based on Idents() did not work. Please provide a cluster field with cluster.field='xxx' from R or --clusterField=xxx if using cbImportSeurat. Possible meta annotation fields are: ", toString(colnames(x = meta)))
-
   if (is.null(x = meta.fields)) {
     meta.fields <- colnames(x = meta)
     #if (length(x = levels(x = Idents(object))) > 1) {
@@ -582,7 +585,7 @@ ExportToCellbrowser <- function(
   }
   if (!is.null(file)) {
     markers.string <- sprintf(
-      'markers = [{"file": "%s", "shortLabel": "Seurat Cluster Markers"}]',
+      'markers = [{"file": "%s", "shortLabel": "Cluster Markers"}]',
       file
     )
   }
@@ -602,15 +605,19 @@ ExportToCellbrowser <- function(
   matrixLabels <- matrixNames
   matrixLabels[matrixLabels=="counts"] <- "read counts"
   matrixLabels[matrixLabels=="scale.data"] <- "scaled"
-  matrices.conf <- sprintf(" {'label':'%s','fileName':'%s_exprMatrix.tsv.gz'}", 
-                           names(slotMatrices), names(slotMatrices))
+  # saveMatrix() writes <prefix>matrix.mtx.gz in MTX mode, <prefix>exprMatrix.tsv.gz otherwise.
+  # use.mtx may also have been switched on above for big matrices, so both file names follow it.
+  matrixFileEnd <- "exprMatrix.tsv.gz"
+  if (use.mtx) {
+    matrixFileEnd <- "matrix.mtx.gz"
+  }
+
+  matrices.conf <- sprintf(" {'label':'%s','fileName':'%s_%s'}",
+                           names(slotMatrices), names(slotMatrices), matrixFileEnd)
 
   matrices.string <- paste0("matrices=[", paste(matrices.conf, collapse = ",\n"), "]" )
 
-  matrixOutPath <- sprintf("%s%sexprMatrix.tsv.gz", firstPrefix, matSep)
-  if (use.mtx) {
-    matrixOutPath <- sprintf("%s%smatrix.mtx.gz", firstPrefix, matSep)
-  }
+  matrixOutPath <- sprintf("%s%s%s", firstPrefix, matSep, matrixFileEnd)
 
   embeddings.conf <- exportImages(object, dir, embeddings.conf)
 
@@ -628,8 +635,7 @@ meta="meta.tsv"
 geneIdType="auto"
 # file with gene,description (one per line) with highlighted genes, called "Dataset Genes" in the user interface
 # quickGenesFile="quickGenes.csv"
-clusterField="%s"
-labelField="%s"
+%s
 enumFields=%s
 %s
 coords=%s
@@ -641,13 +647,22 @@ coords=%s
 
   coords.string <- paste0( "[", paste(embeddings.conf, collapse = ",\n"), "]" )
 
+  # a NULL cluster.field passed to sprintf() would make the whole config come out empty
+  if (is.null(x = cluster.field)) {
+    cluster.string <- paste0(
+      "# No cluster field was given to cbImportSeurat. Uncomment these two lines and set them to one of:\n# ",
+      toString(colnames(x = meta)), "\n",
+      '#clusterField="CHANGE_ME"\n#labelField="CHANGE_ME"')
+  } else {
+    cluster.string <- sprintf('clusterField="%s"\nlabelField="%s"', cluster.field, cluster.field)
+  }
+
   config <- sprintf(
     config,
     dataset.name,
     matrixOutPath,
     matrices.string,
-    cluster.field,
-    cluster.field,
+    cluster.string,
     enum.string,
     markers.string,
     coords.string

{cellbrowser-1.2.20 → cellbrowser-1.2.22}/src/cbPyLib/cellbrowser/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-07-28T16:08:57-0700",
+ "date": "2026-10-30T20:38:46-0700",
  "dirty": false,
  "error": null,
- "full-revisionid": "56488a286184c29ffd35fbb03d6e4a224d64cd80",
- "version": "1.2.20"
+ "full-revisionid": "cf49415184a7f13f66566c4137051f700c29e5b9",
+ "version": "1.2.22"
 }
 '''  # END VERSION_JSON
 

{cellbrowser-1.2.20 → cellbrowser-1.2.22}/src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css

@@ -13,18 +13,42 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         /*border-bottom: 1px solid black; */
 }
 
+/* fixed to the window and filling all of it: the page underneath can be a few pixels taller
+ * than the window, and a box positioned on the page scrolled with it and showed a strip below.
+ * The title bar and the controls stay put, only #tpExprViewPlot scrolls. */
 #tpExprView {
-        position: absolute;
+        position: fixed;
         z-index: 600;
-        display: block;
+        display: flex;
+        flex-direction: column;
         background-color: white;
-        top: 1%;
-        left: 1%;
-        height: 99%;
-        width: 99%;
-        border: 1px solid grey;
-        overflow-y: auto;
+        top: 0;
+        left: 0;
+        right: 0;
+        bottom: 0;
+        overflow: hidden;
+}
+
+/* dot plot hover box, see exprTipShow() */
+#tpExprTip {
+        display: none;
+        position: fixed;
+        z-index: 700;
+        pointer-events: none;
+        white-space: nowrap;
+        background-color: white;
+        color: black;
+        border: 1px solid #aaa;
+        border-radius: 4px;
+        box-shadow: 0 2px 6px rgba(0,0,0,0.2);
+        padding: 6px 9px;
+        font-size: 13px;
+        line-height: 1.4;
 }
+.tpExprTipTitle { font-weight: bold; font-size: 14px; }
+
+/* the hovered dot's row label and gene name */
+#tpExprDotPlot .tpExprHi { font-weight: bold; fill: #1a5fb4; }
 
 #tpExprViewHeader {
         display: flex;
@@ -35,6 +59,12 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
         padding-bottom: 6px;
 }
 
+/* dot plot controls while a load is running, see exprSetBusy() */
+#tpExprViewHeader.tpExprBusy {
+        opacity: 0.5;
+        pointer-events: none;
+}
+
 .hasTooltip {
         display: inline-flex;
         align-items: center;
@@ -110,24 +140,51 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 
 .tpExprHeaderRow { display: flex; align-items: center; gap: 8px; flex-basis: 100%; }
 .tpExprFilterWrap { position: relative; display: inline-block; }
+/* sits immediately left of the "All" button on the split/subsplit rows, so the
+ * button reads as a filter rather than an unlabelled dropdown */
+.tpExprFilterLabel { margin-bottom: 0; margin-left: 6px; }
 .tpExprFilterBtn { height: 25px; font-size: 13px; border: 1px solid #ccc; background: white; cursor: pointer; padding: 0 8px; border-radius: 3px; }
 .tpExprFilterPanel { position: absolute; top: 27px; left: 0; background: white; border: 1px solid #ccc; border-radius: 3px; z-index: 10001; padding: 4px 8px; max-height: 220px; overflow-y: auto; min-width: 150px; box-shadow: 0 2px 6px rgba(0,0,0,0.15); }
 .tpExprFilterItem label { display: block; padding: 1px 0; cursor: pointer; white-space: nowrap; font-size: 13px; }
 .tpExprFilterAll { border-bottom: 1px solid #eee; margin-bottom: 4px; padding-bottom: 3px; font-size: 13px; }
 #tpGeneExprSubsplitLabel { margin-left: 6px; margin-right: 6px; margin-bottom: 0; }
 
+/* takes the space below the controls and scrolls both ways, so a dot plot with many genes or rows
+ * can be scrolled while the controls above it stay in view */
 #tpExprViewPlot {
         display:flex;
         flex-direction: row;
         flex-flow: wrap;
+        align-items: flex-start;
+        align-content: flex-start;
         padding-top:10px;
+        flex: 1;
+        min-height: 0;
+        overflow: auto;
+}
+
+/* a flex item can shrink, so a dot plot with many genes was squeezed to the window width and its
+ * right side cut off. Keep its full width so #tpExprViewPlot can scroll sideways instead. */
+#tpExprViewPlot > svg {
+        flex-shrink: 0;
 }
 
 #tpExprViewContent {
         padding: 6px;
+        flex: 1;
+        min-height: 0;
+        display: flex;
+        flex-direction: column;
+}
+
+#tpExprPerturbRow label {
+        margin-left: 6px;
+        margin-right: 6px;
+        margin-bottom: 0;
 }
 
 #tpGeneExprLabel {
+        margin-left: 6px;
         margin-right: 6px;
         margin-bottom: 0;
 }
@@ -337,8 +394,14 @@ section { font-weight: bold; padding-top: 5px; padding-bottom: 5px }
 }
 .progress-label {
         position: absolute;
-        left: 50%;
+        left: 0;
+        right: 0;
         top: 4px;
+        padding: 0 8px;
+        text-align: center;
+        white-space: nowrap;
+        overflow: hidden;
+        text-overflow: ellipsis;
         font-weight: bold;
         /*text-shadow: 1px 1px 0 #fff;*/
 }
@@ -847,3 +910,239 @@ th[role=columnheader]:not(.no-sort):hover:after {
 /* dataset search result highlighting */
 .tpDatasetLabel mark { background: #fff176; color: inherit; padding: 0 1px; border-radius: 2px; }
 .list-group-item.active .tpDatasetLabel mark { background: #ffe57f; }
+
+/* ============================================================
+   Differential Expression feature (Redmine #24912)
+   New surfaces only. A/B group colors are load-bearing (do not
+   swap without preserving warm-vs-cool contrast). Accent maps to
+   the Cell Browser primary (#337ab7).
+   ============================================================ */
+:root {
+  --tpDeAccent: #337ab7;
+  --tpDeA: #c2603a; --tpDeAtint: #fbf1ec; --tpDeAborder: #eccdbe; --tpDeAtext: #a94c2c; --tpDeAmuted: #9a7f70;
+  --tpDeB: #42559f; --tpDeBtint: #eef0f9; --tpDeBborder: #c6cce8; --tpDeBtext: #3a4a8c; --tpDeBmuted: #77809f;
+  --tpDeCard: #fff; --tpDeCardBorder: #e2e0da; --tpDeInk: #23262b; --tpDeMuted: #6b6f76; --tpDeTert: #8b8f96;
+  --tpDeTrack: #eceae4; --tpDeHair: #e7e5df;
+}
+/* builder lives inside the sidebar Tools tab; flows normally, plain white bg
+   and the default UI font, so it matches the rest of the sidebar */
+#tpDeBuilder { background:#fff; font-size:13px; color:var(--tpDeInk);
+  font-family:Arial,Helvetica,sans-serif; }
+#tpDeBuilder .tpDeHead { padding:11px 4px 11px; border-bottom:1px solid var(--tpDeHair); position:relative; }
+#tpDeBuilder .tpDeTitle { font-size:15px; font-weight:600; letter-spacing:-0.01em; }
+#tpDeBuilder .tpDeSub { font-size:13px; color:var(--tpDeTert); margin-top:2px; }
+#tpDeBuilder .tpDeClose { position:absolute; right:2px; top:9px; font-size:18px; color:var(--tpDeTert);
+  cursor:pointer; line-height:1; padding:2px 5px; border-radius:4px; }
+#tpDeBuilder .tpDeClose:hover { color:var(--tpDeInk); background:#ece9e2; }
+/* the body scrolls when the group lists get long (e.g. after 'swap' materializes
+   all-other-cells), mirroring #tpMetaPanel on the Annotation tab */
+#tpDeBuilder .tpDeBody { padding:12px 2px 16px; display:flex; flex-direction:column; gap:10px;
+  max-height:calc(100vh - 165px); overflow-y:auto; overflow-x:hidden; }
+
+/* which group legend clicks are assigned to */
+.tpDeTargetRow { display:flex; align-items:center; gap:8px; }
+.tpDeTargetRow .tpDeTargetLabel { font-size:13px; color:var(--tpDeMuted); white-space:nowrap; }
+/* "Compare by" field selector at the top of the builder */
+.tpDeFieldRow { display:flex; align-items:center; gap:8px; margin-bottom:2px; }
+.tpDeFieldRow .tpDeFieldLabel { font-size:13px; color:var(--tpDeMuted); white-space:nowrap; }
+.tpDeFieldRow .tpDeField { flex:1 1 0; min-width:0; font-size:13px; padding:4px 5px;
+  border:1px solid var(--tpDeCardBorder); border-radius:5px; background:#fff; }
+/* in-builder clickable value list (assign to A/B without the far-right legend) */
+.tpDeValHead { display:flex; align-items:baseline; justify-content:space-between; gap:6px; margin-top:8px; }
+.tpDeValTo { font-size:12px; font-weight:600; letter-spacing:0.02em; }
+.tpDeValTot { font-size:12px; font-family:monospace; color:var(--tpDeTert); }
+.tpDeValFilter { width:100%; box-sizing:border-box; font-size:13px; padding:5px 8px; margin-top:4px;
+  border:1px solid var(--tpDeCardBorder); border-radius:5px; }
+/* flex:none stops the builder's flex column from shrinking this to 1-2 rows on a
+   short window; it holds its height (up to 40vh) and the builder scrolls instead */
+.tpDeValList { flex:none; max-height:305px; min-height:150px; overflow-y:auto; margin-top:5px;
+  background:#fff; border:1px solid var(--tpDeCardBorder); border-radius:5px; }
+.tpDeValRow { display:flex; align-items:center; gap:8px; padding:6px 10px; cursor:pointer;
+  font-size:13px; border-bottom:1px solid #f1eee7; }
+.tpDeValRow:last-child { border-bottom:none; }
+.tpDeValRow:hover { background:#f0ece4; }
+.tpDeValRow.tpDeValOn:hover { filter:brightness(0.97); }
+.tpDeValDot { width:11px; height:11px; border-radius:50%; flex:none; }
+.tpDeValLbl { flex:1 1 auto; min-width:0; overflow:hidden; text-overflow:ellipsis; white-space:nowrap; }
+.tpDeValN { font-size:11px; font-family:monospace; color:var(--tpDeMuted); }
+.tpDeValBadge { flex:none; width:16px; height:16px; line-height:16px; text-align:center;
+  font-size:11px; font-weight:600; color:#fff; border-radius:3px; }
+.tpDeValBadge.tpDeValBadgeEmpty { background:transparent; }
+.tpDeValEmpty { padding:10px; font-size:12px; color:var(--tpDeTert); text-align:center; }
+.tpDeCard.tpDeActive { border-color:var(--tpDeAccent); box-shadow:0 0 0 1px var(--tpDeAccent); }
+
+.tpDeCard { background:var(--tpDeCard); border:1px solid var(--tpDeCardBorder); border-radius:7px; padding:11px 11px 12px; }
+.tpDeCardHead { display:flex; align-items:center; gap:7px; margin-bottom:9px; }
+.tpDeDot { width:9px; height:9px; border-radius:50%; flex:none; }
+.tpDeCardLabel { font-size:13px; font-weight:600; letter-spacing:0.02em; }
+.tpDeCount { margin-left:auto; font-size:13px; font-family:monospace; color:var(--tpDeMuted); }
+.tpDeCount.tpDeWarn { color:#b4522c; }
+.tpDeHint { font-size:13px; color:var(--tpDeMuted); line-height:1.5; padding:6px 8px; border:1px dashed var(--tpDeCardBorder); border-radius:5px; }
+.tpDeChips { display:flex; flex-wrap:wrap; gap:5px; }
+.tpDeChip { display:inline-flex; align-items:center; gap:6px; border-radius:20px; padding:3px 4px 3px 8px; font-size:13px; border:1px solid; }
+.tpDeChip .tpDeChipDot { width:7px; height:7px; border-radius:50%; flex:none; }
+.tpDeChip .tpDeChipN { font-size:12px; font-family:monospace; }
+.tpDeChip .tpDeChipX { cursor:pointer; font-size:13px; padding:0 2px; border-radius:50%; }
+.tpDeFilterRow { display:flex; gap:6px; margin-top:9px; }
+/* min-width:0 lets the selects shrink instead of spilling past the sidebar when
+   an option label is long (e.g. "subset clusters") */
+.tpDeFilterRow select { flex:1 1 0; min-width:0; max-width:100%; font-size:13px; padding:4px 5px; border:1px solid var(--tpDeCardBorder); border-radius:5px; background:#fff; }
+/* selected filter values (multi-value) shown as removable chips */
+.tpDeFilterChips { display:flex; flex-wrap:wrap; gap:4px; margin-top:5px; }
+.tpDeFilterChip { display:inline-flex; align-items:center; gap:5px; font-size:12px; background:#efece5;
+  border:1px solid var(--tpDeCardBorder); border-radius:12px; padding:2px 4px 2px 8px; }
+.tpDeFilterChip .tpDeFilterChipX { cursor:pointer; font-size:13px; line-height:1; padding:0 3px; border-radius:50%; color:var(--tpDeTert); }
+.tpDeFilterChip .tpDeFilterChipX:hover { color:var(--tpDeInk); background:#ddd8cf; }
+
+.tpDeSwap { display:flex; align-items:center; gap:8px; }
+.tpDeSwap .tpDeSwapLine { flex:1; height:1px; background:var(--tpDeHair); }
+.tpDeSwapBtn { font-size:12px; color:var(--tpDeTert); border:1px solid var(--tpDeCardBorder); background:#fff;
+  border-radius:20px; padding:3px 10px; cursor:pointer; }
+.tpDeSwapBtn:hover { border-color:var(--tpDeAccent); color:var(--tpDeAccent); }
+
+.tpDeSeg { display:flex; background:#efece5; border-radius:5px; padding:2px; margin-bottom:9px; }
+.tpDeSeg button { flex:1; padding:5px 0; font-size:13px; border:none; background:none; border-radius:4px; cursor:pointer; color:var(--tpDeMuted); }
+.tpDeSeg button.tpDeSegOn { background:#fff; font-weight:600; color:var(--tpDeInk); box-shadow:0 1px 2px rgba(0,0,0,0.07); }
+.tpDeRestNote { font-size:13px; color:var(--tpDeTert); line-height:1.5; }
+
+.tpDeSettings .tpDeSettingsHead { display:flex; align-items:center; padding:4px 11px; cursor:pointer; }
+.tpDeSettings .tpDeSettingsHead b { font-size:13px; font-weight:600; }
+.tpDeSettings .tpDeSummary { margin-left:auto; font-size:12px; font-family:monospace; color:var(--tpDeMuted); }
+.tpDeSettingsBody { padding:1px 11px 6px; border-top:1px solid var(--tpDeHair); }
+.tpDeSetRow { display:flex; align-items:center; gap:9px; margin-top:4px; }
+.tpDeSetRow label { flex:1 1 auto; min-width:0; font-size:13px; }
+.tpDeSetRow select, .tpDeSetRow input { flex:0 1 150px; min-width:0; max-width:150px; font-size:13px; padding:3px 5px; border:1px solid var(--tpDeCardBorder); border-radius:4px; }
+.tpDeFoot { font-size:11px; color:var(--tpDeMuted); margin-top:5px; }
+
+.tpDeBanner { background:#fdf3ed; border:1px solid #efd0bc; border-radius:6px; padding:9px 11px; font-size:13px; color:#8a4a26; line-height:1.5; }
+.tpDeRunRow { display:flex; gap:8px; }
+.tpDeRun { flex:1; padding:9px 12px; border-radius:6px; font-size:14px; font-weight:600; color:#fff; background:var(--tpDeAccent); border:none; cursor:pointer; }
+.tpDeRun:disabled { background:#cfccc5; color:#8b8f96; cursor:default; }
+.tpDeReset { padding:9px 12px; border:1px solid var(--tpDeCardBorder); background:#fff; border-radius:6px; cursor:pointer; font-size:14px; }
+
+.tpDeRecentLabel { font-size:12px; font-weight:600; text-transform:uppercase; letter-spacing:0.06em; color:var(--tpDeTert); margin-top:6px; }
+.tpDeRecent { padding:7px 9px; border:1px solid var(--tpDeCardBorder); border-radius:5px; background:#fff; margin-bottom:5px; cursor:pointer; }
+.tpDeRecent:hover { border-color:var(--tpDeAccent); }
+.tpDeRecent .tpDeRecentTitle { font-size:13px; line-height:1.4; }
+.tpDeRecent .tpDeRecentSub { font-size:12px; font-family:monospace; color:var(--tpDeMuted); }
+
+/* collapsible comparison-list sections (Saved / Recent) */
+.tpDeListSec { margin-top:6px; }
+.tpDeListHead { font-size:12px; font-weight:600; text-transform:uppercase; letter-spacing:0.06em;
+  color:var(--tpDeTert); cursor:pointer; user-select:none; padding:2px 0; }
+.tpDeListHead:hover { color:var(--tpDeInk); }
+.tpDeListCaret { display:inline-block; width:12px; color:var(--tpDeMuted); }
+.tpDeListBody { margin-top:4px; }
+
+/* saved comparisons: like a recent row, plus Share / delete controls */
+.tpDeSaved { display:flex; align-items:center; gap:6px; padding:7px 9px; border:1px solid var(--tpDeCardBorder);
+  border-radius:5px; background:#fff; margin-bottom:5px; }
+.tpDeSaved:hover { border-color:var(--tpDeAccent); }
+.tpDeSaved .tpDeSavedMain { flex:1 1 auto; min-width:0; cursor:pointer; }
+.tpDeSaved .tpDeRecentTitle { font-size:13px; line-height:1.4; overflow:hidden; text-overflow:ellipsis; white-space:nowrap; }
+.tpDeSaved .tpDeRecentSub { font-size:12px; font-family:monospace; color:var(--tpDeMuted); }
+.tpDeSavedAct { flex:none; cursor:pointer; color:var(--tpDeTert); border-radius:4px; padding:1px 5px; user-select:none; }
+.tpDeSavedShare { font-size:12px; }
+.tpDeSavedDel { font-size:15px; line-height:1; }
+.tpDeSavedAct:hover { color:var(--tpDeAccent); background:#ece9e2; }
+
+/* "Save to account" shown greyed when signed out (still clickable -> opens sign-in) */
+.ui-dialog-buttonpane button.tpDeBtnDisabled { opacity:0.5; }
+.ui-dialog-buttonpane button.tpDeBtnDisabled:hover { opacity:0.65; }
+
+/* transient confirmation toast (e.g. after saving a comparison) */
+.tpDeToast { position:fixed; left:50%; bottom:40px; transform:translateX(-50%); z-index:100000;
+  background:rgba(35,38,43,0.92); color:#fff; font-size:13px; padding:8px 16px; border-radius:5px;
+  box-shadow:0 2px 10px rgba(0,0,0,0.25); pointer-events:none; }
+
+/* legend A/B buttons (added while builder open) */
+.tpDeLegBtns { display:inline-flex; gap:3px; margin-left:6px; vertical-align:middle; }
+.tpDeLegBtn { width:19px; height:19px; border-radius:4px; font-size:11px; font-weight:600; line-height:17px;
+  text-align:center; border:1px solid #d6d3cc; background:#fff; color:#b7b4ad; cursor:pointer; padding:0; }
+.tpDeLegBtn.tpDeLegA.tpDeOn { background:var(--tpDeA); border-color:var(--tpDeA); color:#fff; }
+.tpDeLegBtn.tpDeLegB.tpDeOn { background:var(--tpDeB); border-color:var(--tpDeB); color:#fff; }
+.tpLegend.tpDeRowA { background:var(--tpDeAtint); border-color:var(--tpDeAborder) !important; }
+.tpLegend.tpDeRowB { background:var(--tpDeBtint); border-color:var(--tpDeBborder) !important; }
+
+/* running overlay confined to the plot area */
+#tpDeRunning { position:absolute; z-index:20; background:rgba(255,255,255,0.72);
+  display:flex; align-items:center; justify-content:center; }
+#tpDeRunning .tpDeRunCard { width:330px; background:#fff; border:1px solid var(--tpDeCardBorder); border-radius:9px;
+  box-shadow:0 16px 42px rgba(10,12,15,0.16); padding:20px 24px; }
+#tpDeRunning .tpDeRunTop { display:flex; align-items:center; gap:10px; font-size:14px; font-weight:600; }
+#tpDeSpinner { width:15px; height:15px; border:2px solid #dcdad3; border-top-color:var(--tpDeAccent);
+  border-radius:50%; animation:tpDeSpin .8s linear infinite; flex:none; }
+@keyframes tpDeSpin { to { transform:rotate(360deg); } }
+#tpDeRunning .tpDeProgTrack { height:5px; background:var(--tpDeTrack); border-radius:3px; margin-top:14px; overflow:hidden; }
+#tpDeRunning .tpDeProgFill { height:100%; width:0; background:var(--tpDeAccent); border-radius:3px; transition:width .3s ease; }
+#tpDeRunning .tpDeStage { margin-top:9px; font-size:13px; font-family:monospace; color:var(--tpDeTert); }
+#tpDeRunning .tpDeCancel { margin-top:12px; text-align:right; }
+#tpDeRunning .tpDeCancel button { font-size:12px; border:1px solid var(--tpDeCardBorder); background:#fff; border-radius:5px; padding:4px 10px; cursor:pointer; }
+
+/* results pop-up (non-modal dialog) */
+#tpDeResults { font-size:13px; color:var(--tpDeInk); font-family:Arial,Helvetica,sans-serif; }
+/* jQuery UI forces Verdana on .ui-widget content; keep the DE dialog on the
+   default UI font (its title bar is part of the widget chrome) */
+.ui-dialog:has(#tpDeResults), .ui-dialog:has(#tpDeResults) .ui-dialog-title { font-family:Arial,Helvetica,sans-serif; }
+#tpDeResults .tpDeResHead { display:flex; align-items:baseline; gap:12px; padding:6px 2px 10px; border-bottom:1px solid var(--tpDeHair); }
+#tpDeResults .tpDeResTitle { font-size:14px; font-weight:600; letter-spacing:-0.01em; }
+#tpDeResults .tpDeResSub { font-size:13px; font-family:monospace; color:var(--tpDeMuted); }
+#tpDeResBody { display:flex; height:100%; }
+#tpDeResTableWrap { flex:1; display:flex; flex-direction:column; border-right:1px solid var(--tpDeHair); min-width:0; overflow-y:auto; }
+#tpDeResVolcano { width:360px; flex:none; padding:8px 12px 10px; overflow-y:auto; }
+.tpDeCtrls { display:flex; align-items:center; gap:8px; padding:8px 4px 6px; }
+.tpDeCtrls input.tpDeGeneFilter { width:150px; font-size:13px; padding:4px 8px; border:1px solid var(--tpDeCardBorder); border-radius:4px; }
+.tpDeCtrls2 { padding:0 4px 8px; border-bottom:1px solid var(--tpDeHair); }
+.tpDeGeneCount { margin-left:auto; font-size:12px; font-family:monospace; color:var(--tpDeTert); }
+/* results table: Bootstrap .table look, matching the cluster-markers pop-up */
+#tpDeTable { margin-bottom:0; }
+#tpDeTable thead th { position:sticky; top:0; background:#fff; cursor:pointer; white-space:nowrap;
+  border-bottom:2px solid #ddd; }
+#tpDeTable thead th.tpDeSortOn { color:var(--tpDeAccent); }
+#tpDeTable td, #tpDeTable th { font-size:13px; padding:5px 7px; white-space:nowrap; }
+#tpDeTable td.tpDeNum, #tpDeTable th.tpDeNum { text-align:right; }
+#tpDeTable tbody tr { cursor:pointer; }
+#tpDeTable tbody tr:hover { background:#f5f5f5; }
+#tpDeTable tbody tr.tpDeRowSel > td { background:#eaf1f8; }
+.tpDeGene { font-family:monospace; font-weight:500; white-space:nowrap; max-width:120px; overflow:hidden; text-overflow:ellipsis; }
+.tpDeGene .tpDeDirDot { display:inline-block; width:6px; height:6px; border-radius:50%; margin-right:6px; vertical-align:middle; }
+.tpDeNum { font-family:monospace; }
+#tpDeResVolcano .tpDeVolHead { display:flex; align-items:baseline; }
+#tpDeResVolcano .tpDeVolTitle { font-size:12px; font-weight:600; letter-spacing:0.04em; text-transform:uppercase; color:var(--tpDeMuted); }
+#tpDeResVolcano .tpDeVolHint { margin-left:auto; font-size:12px; color:var(--tpDeTert); }
+.tpDeEmpty { display:flex; flex-direction:column; align-items:center; justify-content:center; gap:9px; height:100%; padding:0 40px; text-align:center; }
+.tpDeEmpty h3 { font-size:15px; font-weight:600; margin:0; }
+.tpDeEmpty p { font-size:14px; color:var(--tpDeTert); line-height:1.6; max-width:520px; }
+.tpDeEmptyBtns { display:flex; gap:8px; margin-top:5px; }
+.tpDeEmptyBtns .tpDeLoosen { background:var(--tpDeAccent); color:#fff; border:none; padding:7px 13px; font-size:13px; border-radius:5px; cursor:pointer; }
+.tpDeEmptyBtns .tpDeEditGroups { background:#fff; border:1px solid var(--tpDeCardBorder); padding:7px 13px; font-size:13px; border-radius:5px; cursor:pointer; }
+
+/* Debug timing bar (?debug=1): fixed strip along the bottom of the window that
+   shows the ms spent in each dataset-load phase. Only created when debug mode is
+   on; see cbTiming() in cellBrowser.js. Dark, monospace, out of the way. */
+#tpDebugBar {
+    position: fixed; left: 0; right: 0; bottom: 0;
+    background: rgba(24,24,24,0.90); color: #d8d8d8;
+    font-family: Menlo, Consolas, monospace; font-size: 13px;
+    padding: 0 14px;
+    border-top: 1px solid #444; z-index: 100000;
+}
+/* one row per timing run: the dataset load, then a DE job. Each scrolls on its
+   own, and the right padding keeps a long row from running under the close box. */
+#tpDebugBar .tpDebugRow {
+    height: 32px; line-height: 32px; white-space: nowrap; overflow-x: auto;
+    padding-right: 26px;
+}
+#tpDebugBar .tpDebugRow + .tpDebugRow { border-top: 1px solid #3a3a3a; }
+#tpDebugBar .tpDebugSeg { margin-right: 20px; }
+#tpDebugBar .tpDebugTag { color: #7fb0ff; font-weight: bold; text-transform: uppercase; letter-spacing: 0.5px; }
+#tpDebugBar .tpDebugLbl { color: #9fd0ff; }
+#tpDebugBar .tpDebugVal { color: #ffd48a; }
+#tpDebugBar .tpDebugTot { color: #9fe6a0; }
+#tpDebugBar .tpDebugGroup { color: #7fb0ff; font-weight: bold; text-transform: uppercase; letter-spacing: 0.5px; }
+#tpDebugBar .tpDebugDraw { color: #f0a0ff; }
+#tpDebugBar .tpDebugClose {
+    position: absolute; right: 12px; top: 0; height: 32px; line-height: 32px;
+    cursor: pointer; color: #aaa; font-weight: bold;
+}
+#tpDebugBar .tpDebugClose:hover { color: #fff; }

cellbrowser-1.2.22/src/cbPyLib/cellbrowser/cbWeb/genes/makeMgiIds.py

@@ -0,0 +1,60 @@
+# Build the mouse gene symbol -> MGI ID table that the marker table uses to link
+# straight to a gene page instead of to a search hit list.
+#
+# Input is the MGI file we already ship for ortholog mapping, cellbrowserData/geneAnnot/
+# mgi_HGNC_homologene_8Dec17.txt, which carries the accession, the symbol and the feature
+# type. Nothing new has to be downloaded.
+#
+# Only protein coding genes are kept. That is 23k of the 70k markers in the file and covers
+# 93% of the symbols in the marker tables we serve, where taking everything would cover 96%
+# for nearly three times the transfer. A symbol that is not in the table falls back to the
+# symbol search, so the genes left out still get a working link.
+#
+# Output is JSON rather than TSV because the server gzips application/json and does not gzip
+# text/tab-separated-values, so the JSON is the smaller of the two over the wire. The "MGI:"
+# prefix is dropped and put back by the browser.
+#
+#   python3 makeMgiIds.py ../../../../../cellbrowserData/geneAnnot/mgi_HGNC_homologene_8Dec17.txt
+#
+# Name the output after the version of the input, so it can be cached forever.
+
+import json, sys, gzip
+from os.path import basename
+
+def main():
+    if len(sys.argv) < 2:
+        sys.exit("usage: makeMgiIds.py <mgi_HGNC_homologene file> [outFname]")
+    inFname = sys.argv[1]
+
+    if len(sys.argv) > 2:
+        outFname = sys.argv[2]
+    else:
+        # mgi_HGNC_homologene_8Dec17.txt -> mgiIds-8Dec17.json
+        stem = basename(inFname).rsplit(".", 1)[0]
+        outFname = "mgiIds-%s.json" % stem.split("_")[-1]
+
+    symToId = {}
+    skipped = 0
+    for i, line in enumerate(open(inFname, encoding="utf8", errors="replace")):
+        if i == 0:
+            continue
+        row = line.rstrip("\n").split("\t")
+        if len(row) < 4:
+            continue
+        mgiId, sym, _, featType = row[0], row[1], row[2], row[3]
+        if not sym or not mgiId.startswith("MGI:"):
+            continue
+        if featType != "protein coding gene":
+            skipped += 1
+            continue
+        symToId[sym] = int(mgiId[4:])
+
+    blob = json.dumps(symToId, separators=(",", ":"), sort_keys=True)
+    with open(outFname, "w") as ofh:
+        ofh.write(blob)
+
+    gzSize = len(gzip.compress(blob.encode(), 9))
+    print("%s: %d protein coding symbols (%d other features skipped)" % (outFname, len(symToId), skipped))
+    print("  %.1f KB, %.1f KB gzipped as the server will send it" % (len(blob)/1024.0, gzSize/1024.0))
+
+main()