Release 7.0.1 (#142)

## What's changed * feat: add get_default_postgres_url utility (#136) * feat: debug log for access_token in oauth security store (#139) * Fix: tooltip bug in violin plot (#140) * Handle null value only columns in raincloud plot (#130)
datavisyn · Jan 10, 2024 · 9167484 · 9167484
2 parents 7682cd9 + a2d31c1
commit 9167484
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diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "visyn_core",
   "description": "Core repository for datavisyn applications.",
-  "version": "7.0.0",
+  "version": "7.0.1",
   "author": {
     "name": "datavisyn GmbH",
     "email": "[email protected]",

diff --git a/src/vis/raincloud/Raincloud.tsx b/src/vis/raincloud/Raincloud.tsx
@@ -20,6 +20,7 @@ import { Circle } from './rain/Circle';
 import { DotPlot } from './rain/DotPlot';
 import { StripPlot } from './rain/StripPlot';
 import { WheatPlot } from './rain/WheatPlot';
+import { InvalidCols } from '../general/InvalidCols';
 
 const margin = {
   top: 0,
@@ -103,6 +104,8 @@ export function Raincloud({
       .rollup({ values: op.mean('values'), ids: op.array_agg('ids') });
   }, [baseTable]);
 
+  const hasData = column.resolvedValues.filter((row) => row.val !== null).length > 0;
+
   return (
     <Box ref={ref} style={{ maxWidth: '100%', maxHeight: '100%', position: 'relative', overflow: 'hidden' }}>
       <Container
@@ -120,70 +123,76 @@ export function Raincloud({
               <text textAnchor="middle" dominantBaseline="middle" x={width / 2} y={15}>
                 {column.info.name}
               </text>
-              <g>
-                {config.cloudType === ECloudType.HEATMAP ? (
-                  <Heatmap width={width} height={height / 2} config={config} numCol={column} />
-                ) : config.cloudType === ECloudType.HISTOGRAM ? (
-                  <Histogram width={width} height={height / 2} config={config} numCol={column} />
-                ) : (
-                  <SplitViolin width={width} height={height / 2} config={config} numCol={column} />
-                )}
-
-                {config.rainType === ERainType.DOTPLOT ? (
-                  <DotPlot
-                    yPos={height / 2}
-                    width={width}
-                    height={height}
-                    config={config}
-                    numCol={column}
-                    circleCallback={circlesCallback}
-                    baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
-                  />
-                ) : config.rainType === ERainType.BEESWARM ? (
-                  <BeeSwarm
-                    baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
-                    yPos={height / 2}
-                    width={width}
-                    height={height / 2}
-                    config={config}
-                    numCol={column}
-                    circleCallback={circlesCallback}
-                  />
-                ) : config.rainType === ERainType.WHEATPLOT ? (
-                  <WheatPlot
-                    yPos={height / 2}
-                    width={width}
-                    height={height / 2}
-                    config={config}
-                    numCol={column}
-                    circleCallback={circlesCallback}
-                    baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
-                  />
-                ) : config.rainType === ERainType.STRIPPLOT ? (
-                  <StripPlot
-                    yPos={height / 2}
-                    width={width}
-                    height={height / 2}
-                    config={config}
-                    numCol={column}
-                    circleCallback={circlesCallback}
-                    baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
-                  />
-                ) : null}
-                {circlesRendered}
-                {config.lightningType === ELightningType.MEAN_AND_DEV ? (
-                  <MeanAndInterval yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
-                ) : config.lightningType === ELightningType.MEAN ? (
-                  <Mean yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
-                ) : config.lightningType === ELightningType.MEDIAN_AND_DEV ? (
-                  <MedianAndInterval yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
-                ) : config.lightningType === ELightningType.BOXPLOT ? (
-                  <Boxplot yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
-                ) : null}
-
-                <XAxis xScale={xScale} vertPosition={height / 2} yRange={null} />
-                <Brush y={height / 2 - 20} x={margin.left} height={40} width={width - margin.left} onBrush={brushCallback} id={column.info.id} />
-              </g>
+              {hasData ? (
+                <g>
+                  {config.cloudType === ECloudType.HEATMAP ? (
+                    <Heatmap width={width} height={height / 2} config={config} numCol={column} />
+                  ) : config.cloudType === ECloudType.HISTOGRAM ? (
+                    <Histogram width={width} height={height / 2} config={config} numCol={column} />
+                  ) : (
+                    <SplitViolin width={width} height={height / 2} config={config} numCol={column} />
+                  )}
+
+                  {config.rainType === ERainType.DOTPLOT ? (
+                    <DotPlot
+                      yPos={height / 2}
+                      width={width}
+                      height={height}
+                      config={config}
+                      numCol={column}
+                      circleCallback={circlesCallback}
+                      baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
+                    />
+                  ) : config.rainType === ERainType.BEESWARM ? (
+                    <BeeSwarm
+                      baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
+                      yPos={height / 2}
+                      width={width}
+                      height={height / 2}
+                      config={config}
+                      numCol={column}
+                      circleCallback={circlesCallback}
+                    />
+                  ) : config.rainType === ERainType.WHEATPLOT ? (
+                    <WheatPlot
+                      yPos={height / 2}
+                      width={width}
+                      height={height / 2}
+                      config={config}
+                      numCol={column}
+                      circleCallback={circlesCallback}
+                      baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
+                    />
+                  ) : config.rainType === ERainType.STRIPPLOT ? (
+                    <StripPlot
+                      yPos={height / 2}
+                      width={width}
+                      height={height / 2}
+                      config={config}
+                      numCol={column}
+                      circleCallback={circlesCallback}
+                      baseTable={config.aggregateRain || column.resolvedValues.length > MAX_NON_AGGREGATED_COUNT ? aggregatedTable : baseTable}
+                    />
+                  ) : null}
+                  {circlesRendered}
+                  {config.lightningType === ELightningType.MEAN_AND_DEV ? (
+                    <MeanAndInterval yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
+                  ) : config.lightningType === ELightningType.MEAN ? (
+                    <Mean yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
+                  ) : config.lightningType === ELightningType.MEDIAN_AND_DEV ? (
+                    <MedianAndInterval yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
+                  ) : config.lightningType === ELightningType.BOXPLOT ? (
+                    <Boxplot yPos={height / 2} width={width} height={height} config={config} numCol={column} baseTable={baseTable} />
+                  ) : null}
+
+                  <XAxis xScale={xScale} vertPosition={height / 2} yRange={null} />
+                  <Brush y={height / 2 - 20} x={margin.left} height={40} width={width - margin.left} onBrush={brushCallback} id={column.info.id} />
+                </g>
+              ) : (
+                <foreignObject width="100%" height="100%">
+                  <InvalidCols headerMessage="Invalid data" bodyMessage="Could not render plot due to all values being null." />
+                </foreignObject>
+              )}
             </g>
           ) : null}
         </svg>

diff --git a/src/vis/violin/ViolinVis.tsx b/src/vis/violin/ViolinVis.tsx
@@ -19,16 +19,40 @@ export function ViolinVis({ config, columns, scales, dimensions, selectedList, s
 
   const [layout, setLayout] = useState<Partial<Plotly.Layout>>(null);
 
-  const onClick = (e: Readonly<PlotlyTypes.PlotSelectionEvent> | null) => {
+  // Filter out null values from traces as null values cause the tooltip to not show up
+  const filteredTraces = useMemo(() => {
+    if (!traces) return null;
+    const indexWithNull = traces.plots?.map(
+      (plot) => (plot?.data.y as PlotlyTypes.Datum[])?.reduce((acc: number[], curr, i) => (curr === null ? [...acc, i] : acc), []) as number[],
+    );
+    const filtered = {
+      ...traces,
+      plots: traces?.plots?.map((p, p_index) => {
+        return {
+          ...p,
+          data: {
+            ...p.data,
+            y: (p.data?.y as PlotlyTypes.Datum[])?.filter((v, i) => !indexWithNull[p_index].includes(i)),
+            x: (p.data?.x as PlotlyTypes.Datum[])?.filter((v, i) => !indexWithNull[p_index].includes(i)),
+            ids: p.data?.ids?.filter((v, i) => !indexWithNull[p_index].includes(i)),
+            transforms: p.data?.transforms?.map(
+              (t) => (t.groups as unknown[])?.filter((v, i) => !indexWithNull[p_index].includes(i)) as Partial<PlotlyTypes.Transform>,
+            ),
+          },
+        };
+      }),
+    };
+    return filtered;
+  }, [traces]);
+
+  const onClick = (e: (Readonly<PlotlyTypes.PlotSelectionEvent> & { event: MouseEvent }) | null) => {
     if (!e || !e.points || !e.points[0]) {
       selectionCallback([]);
       return;
     }
 
-    // @ts-ignore
     const shiftPressed = e.event.shiftKey;
-    // @ts-ignore
-    const eventIds = e.points[0]?.fullData.ids;
+    const eventIds = (e.points[0] as Readonly<PlotlyTypes.PlotSelectionEvent>['points'][number] & { fullData: { ids: string[] } })?.fullData.ids;
 
     // Multiselect enabled
     if (shiftPressed) {
@@ -78,7 +102,7 @@ export function ViolinVis({ config, columns, scales, dimensions, selectedList, s
   }, [clearTimeoutValue]);
 
   useEffect(() => {
-    if (!traces) {
+    if (!filteredTraces) {
       return;
     }
 
@@ -99,12 +123,12 @@ export function ViolinVis({ config, columns, scales, dimensions, selectedList, s
       },
       clickmode: 'event+select',
       autosize: true,
-      grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' },
+      grid: { rows: filteredTraces.rows, columns: filteredTraces.cols, xgap: 0.3, pattern: 'independent' },
       shapes: [],
     };
 
-    setLayout((prev) => ({ ...prev, ...beautifyLayout(traces, innerLayout, prev, true) }));
-  }, [traces]);
+    setLayout((prev) => ({ ...prev, ...beautifyLayout(filteredTraces, innerLayout, prev, true) }));
+  }, [filteredTraces]);
 
   return (
     <Stack
@@ -120,10 +144,10 @@ export function ViolinVis({ config, columns, scales, dimensions, selectedList, s
         },
       }}
     >
-      {traceStatus === 'success' && layout && traces?.plots.length > 0 ? (
+      {traceStatus === 'success' && layout && filteredTraces?.plots.length > 0 ? (
         <PlotlyComponent
           divId={`plotlyDiv${id}`}
-          data={[...traces.plots.map((p) => p.data), ...traces.legendPlots.map((p) => p.data)]}
+          data={[...filteredTraces.plots.map((p) => p.data), ...filteredTraces.legendPlots.map((p) => p.data)]}
           layout={layout}
           config={{ responsive: true, displayModeBar: false }}
           useResizeHandler
@@ -139,7 +163,7 @@ export function ViolinVis({ config, columns, scales, dimensions, selectedList, s
           }}
         />
       ) : traceStatus !== 'pending' && traceStatus !== 'idle' && layout ? (
-        <InvalidCols headerMessage={traces?.errorMessageHeader} bodyMessage={traceError?.message || traces?.errorMessage} />
+        <InvalidCols headerMessage={filteredTraces?.errorMessageHeader} bodyMessage={traceError?.message || filteredTraces?.errorMessage} />
       ) : null}
     </Stack>
   );

diff --git a/visyn_core/security/store/oauth2_security_store.py b/visyn_core/security/store/oauth2_security_store.py
@@ -24,7 +24,7 @@ def load_from_request(self, req: Request):
             # Get token data from header
             access_token = req.headers.get(token_field)
             if access_token:
-                # Try to decode the oidc data jwt
+                _log.debug(f"Try to decode the oidc data jwt with access token: {access_token}")
                 user = jwt.decode(access_token, options={"verify_signature": False})
 
                 # Go through all the fields we want to check for the user id

diff --git a/visyn_core/settings/model.py b/visyn_core/settings/model.py
@@ -205,6 +205,10 @@ class VisynCoreSettings(BaseModel):
 
 class GlobalSettings(BaseSettings):
     env: Literal["development", "production"] = "production"
+    ci: bool = False
+    """
+    Set to true in CI environments like Github Actions.
+    """
     secret_key: str = "VERY_SECRET_STUFF_T0IB84wlQrdMH8RVT28w"
 
     # JWT options mostly inspired by flask-jwt-extended: https://flask-jwt-extended.readthedocs.io/en/stable/options/#general-options

diff --git a/visyn_core/settings/utils.py b/visyn_core/settings/utils.py
@@ -28,3 +28,18 @@ def load_config_file(path: str) -> dict[str, Any]:
     """
     with codecs.open(path, "r", "utf-8") as fi:
         return jsoncfg.loads(fi.read()) or {}
+
+
+def get_default_postgres_url(
+    *,
+    user: str = "admin",
+    password: str = "admin",
+    host: str | None = os.getenv("POSTGRES_HOSTNAME"),
+    host_fallback: str = "localhost",
+    port: int = 5432,
+    database: str = "db",
+) -> str:
+    """
+    Returns a default postgres url, including the default values for `user`, `password`, `host`, `port` and `database`.
+    """
+    return f"postgresql://{user}:{password}@{host or host_fallback}:{port}/{database}"