Merge main into sweep/add-readme-dev-docs

CNAG-Biomedical-Informatics · Sep 1, 2023 · 6ffac24 · 6ffac24
2 parents 61ae165 + cfe8201
commit 6ffac24
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Showing 45 changed files with 208 additions and 209 deletions.
diff --git a/convertPheno_client/cypress/e2e/home.spec.js b/convertPheno_client/cypress/e2e/home.spec.js
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/getKCTokens.sh b/convertPheno_client/getKCTokens.sh
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_client/replace_env_vars.sh b/convertPheno_client/replace_env_vars.sh
@@ -6,7 +6,7 @@
 #
 #   Last Modified: Apr/28/2023
 #
-#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+#   Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 #
 #   License: GPL-3.0 license
 

diff --git a/convertPheno_client/src/code/App.jsx b/convertPheno_client/src/code/App.jsx
@@ -5,13 +5,19 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */
 
 import React, { useEffect, useContext, useMemo, useState } from "react";
-import { Navigate, Route, Routes, useNavigate, useParams } from "react-router-dom";
+import {
+  Navigate,
+  Route,
+  Routes,
+  useNavigate,
+  useParams,
+} from "react-router-dom";
 import { ErrorBoundary } from "react-error-boundary";
 import { Box, Grid } from "@mui/material";
 import { useTheme, ThemeProvider, createTheme } from "@mui/material/styles";
@@ -99,22 +105,22 @@ function renderRoutes() {
   ));
 }
 
-function AuthenticatedRoute ({ element: Component, path, security }) {
+function AuthenticatedRoute({ element: Component, path, security }) {
   const navigate = useNavigate();
   const isAuthenticated = security === "false" || auth.user.authenticated;
   const params = useParams();
 
   useEffect(() => {
     if (!isAuthenticated) {
       if ("jobId" in params) {
-        path = `${ path }/${ params.jobId }`;
+        path = `${path}/${params.jobId}`;
       }
       navigate("/login", { state: { redirect: path } });
     }
   }, [auth.user.authenticated, navigate]);
 
   return isAuthenticated ? <Component /> : null;
-};
+}
 
 function App() {
   const theme = useTheme();

diff --git a/convertPheno_client/src/code/Auth.js b/convertPheno_client/src/code/Auth.js
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/Login.jsx b/convertPheno_client/src/code/Login.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */
@@ -20,7 +20,7 @@ import Home from "./views/home/Home";
 
 const kcConfig =
   process.env.NODE_ENV === "production"
-    ? JSON.parse(window.REACT_APP_KC_CONFIG.replace(/'/g, "\""))
+    ? JSON.parse(window.REACT_APP_KC_CONFIG.replace(/'/g, '"'))
     : JSON.parse(import.meta.env.VITE_KC_CONFIG);
 
 const keycloakConfig = {

diff --git a/convertPheno_client/src/code/Main.jsx b/convertPheno_client/src/code/Main.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/apis.js b/convertPheno_client/src/code/apis.js
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/header/Header.jsx b/convertPheno_client/src/code/header/Header.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/views/about/About.tsx b/convertPheno_client/src/code/views/about/About.tsx
@@ -5,7 +5,7 @@
 
   Last Modified: Jun/21/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx b/convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...version/ components/clinicalData/components/columnsTreeViewModal/ColumnsTreeViewModal.jsx b/...version/ components/clinicalData/components/columnsTreeViewModal/ColumnsTreeViewModal.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...nt/src/code/views/conversion/ components/clinicalData/components/dataGrid/CopyOnClick.jsx b/...nt/src/code/views/conversion/ components/clinicalData/components/dataGrid/CopyOnClick.jsx
@@ -5,13 +5,14 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */
 
 import React, { useState, useRef } from "react";
 import { Button, Popover, Tooltip, Typography } from "@mui/material";
+import ValueWithTooltip from "./ValueWithTooltip";
 
 const UnstyledButton = ({ onClick, children }) => {
   return (
@@ -84,62 +85,6 @@ const getValue = (props) => {
   );
 };
 
-const ValueWithTooltip = ({ value, ontology_id, url }) => {
-  const [isTooltipOpen, setIsTooltipOpen] = useState(false);
-  const tooltipTimeout = useRef({ current: null });
-
-  console.log("value", value);
-  console.log("ontology_id", ontology_id);
-  console.log("url", url);
-
-  const handleMouseOver = (value) => {
-    if (value === "NA") {
-      return;
-    }
-    setIsTooltipOpen(true);
-    clearTimeout(tooltipTimeout.current);
-  };
-
-  const handleMouseOut = () => {
-    tooltipTimeout.current = setTimeout(() => {
-      setIsTooltipOpen(false);
-    }, 1000);
-  };
-
-  const handleLinkClick = () => {
-    clearTimeout(tooltipTimeout.current);
-    window.open(url, "_blank");
-  };
-
-  return (
-    <Tooltip
-      open={isTooltipOpen}
-      title={
-        <span>
-          Click to open{" "}
-          <a
-            href={url}
-            target="_blank"
-            rel="noopener noreferrer"
-            onClick={handleLinkClick}
-          >
-            {ontology_id}
-          </a>
-        </span>
-      }
-      placement="bottom"
-    >
-      <span
-        onMouseOver={() => handleMouseOver(value)}
-        onMouseOut={handleMouseOut}
-        style={{ marginRight: "5px", cursor: "pointer" }}
-      >
-        {value}
-      </span>
-    </Tooltip>
-  );
-};
-
 const PopoverButton = ({
   children,
   onClick,

diff --git a/...lient/src/code/views/conversion/ components/clinicalData/components/dataGrid/DataGrid.jsx b/...lient/src/code/views/conversion/ components/clinicalData/components/dataGrid/DataGrid.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...c/code/views/conversion/ components/clinicalData/components/dataGrid/ValueWithTooltip.jsx b/...c/code/views/conversion/ components/clinicalData/components/dataGrid/ValueWithTooltip.jsx
@@ -0,0 +1,68 @@
+/**
+  renders the value of a cell in the data grid with a tooltip that shows the ontology id and a link to the ontology term
+
+  This file is part of convert-pheno-ui
+
+  Last Modified: Sep/1/2023
+
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
+
+  License: GPL-3.0 license
+*/
+
+import React, { useState, useRef } from "react";
+import { Tooltip } from "@mui/material";
+
+export default function ValueWithTooltip(props) {
+  const { value, ontology_id, url } = props;
+
+  const [isTooltipOpen, setIsTooltipOpen] = useState(false);
+  const tooltipTimeout = useRef({ current: null });
+
+  const handleMouseOver = (value) => {
+    if (value === "NA") {
+      return;
+    }
+    setIsTooltipOpen(true);
+    clearTimeout(tooltipTimeout.current);
+  };
+
+  const handleMouseOut = () => {
+    tooltipTimeout.current = setTimeout(() => {
+      setIsTooltipOpen(false);
+    }, 1000);
+  };
+
+  const handleLinkClick = () => {
+    clearTimeout(tooltipTimeout.current);
+    window.open(url, "_blank");
+  };
+
+  return (
+    <Tooltip
+      open={isTooltipOpen}
+      title={
+        <span>
+          Click to open{" "}
+          <a
+            href={url}
+            target="_blank"
+            rel="noopener noreferrer"
+            onClick={handleLinkClick}
+          >
+            {ontology_id}
+          </a>
+        </span>
+      }
+      placement="bottom"
+    >
+      <span
+        onMouseOver={() => handleMouseOver(value)}
+        onMouseOut={handleMouseOut}
+        style={{ marginRight: "5px", cursor: "pointer" }}
+      >
+        {value}
+      </span>
+    </Tooltip>
+  );
+}
diff --git a/...c/code/views/conversion/ components/clinicalData/components/queryBuilder/QueryBuilder.jsx b/...c/code/views/conversion/ components/clinicalData/components/queryBuilder/QueryBuilder.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...e/views/conversion/ components/clinicalData/components/queryBuilder/components/DndBox.jsx b/...e/views/conversion/ components/clinicalData/components/queryBuilder/components/DndBox.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...iews/conversion/ components/clinicalData/components/queryBuilder/components/DndTarget.jsx b/...iews/conversion/ components/clinicalData/components/queryBuilder/components/DndTarget.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...ews/conversion/ components/clinicalData/components/queryBuilder/hooks/useQueryBuilder.jsx b/...ews/conversion/ components/clinicalData/components/queryBuilder/hooks/useQueryBuilder.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...t/src/code/views/conversion/ components/clinicalData/components/simpleTabs/SimpleTabs.jsx b/...t/src/code/views/conversion/ components/clinicalData/components/simpleTabs/SimpleTabs.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/views/conversion/ components/clinicalData/hooks/queryDb.jsx b/convertPheno_client/src/code/views/conversion/ components/clinicalData/hooks/queryDb.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx b/convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/...heno_client/src/code/views/conversion/ components/submission/components/arrows/Arrows.jsx b/...heno_client/src/code/views/conversion/ components/submission/components/arrows/Arrows.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */

diff --git a/.../views/conversion/ components/submission/components/fileMappingModal/FileMappingModal.jsx b/.../views/conversion/ components/submission/components/fileMappingModal/FileMappingModal.jsx
@@ -5,7 +5,7 @@
 
   Last Modified: Apr/28/2023
 
-  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG (Ivo.leist@cnag.crg.eu)
+  Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])
 
   License: GPL-3.0 license
 */