Merge branch 'main' into VLE/KBE-34/routing_of_merging_data

api/__init__.py

@@ -46,7 +46,7 @@
     download_database_for_eys_gene,
 
     # Functions for storing databases
-    store_database_for_eys_gene
+    download_selected_database_for_eys_gene
 )
 
 # DATA REFACTORING IMPORT

api/data/__init__.py

@@ -33,6 +33,26 @@
   GNOMAD_PATH,
 )
 
+# DATA COLLECTION IMPORT
+from .downloading import (
+    # Custom exceptions
+    BadResponseException,
+    DownloadError,
+
+    # Custom utility functions
+    get_file_from_url,
+
+    # Functions for downloading databases
+    download_lovd_database_for_eys_gene,
+    download_genes_lovd,
+    download_database_for_eys_gene,
+    download_data_from_gnomad_eys,
+
+    # Functions for storing databases
+    download_selected_database_for_eys_gene
+
+)
+
 # DATA REFACTORING IMPORT
 from .refactoring import (
     # Functions for refactoring data

api/data/constants.py

@@ -8,6 +8,7 @@
 LOVD_FILE_URL = "https://databases.lovd.nl/shared/download/all/gene/"
 LOVD_FILE_URL_EYS = LOVD_FILE_URL + "EYS"
 STORE_AS_LOVD = "../data/lovd/lovd_data.txt"
+STORE_AS_GNOMAD = "../data/gnomad/gnomad_data.csv"
 
 GNOMAD_URL = "https://gnomad.broadinstitute.org/gene"
 GNOMAD_URL_EYS = "https://gnomad.broadinstitute.org/gene/ENSG00000188107?dataset=gnomad_r4"

api/data/downloading.py

@@ -18,7 +18,8 @@
                         LOVD_PATH,
                         DATABASES_DOWNLOAD_PATHS,
                         LOVD_FILE_URL_EYS,
-                        STORE_AS_LOVD)
+                        STORE_AS_LOVD,
+                        STORE_AS_GNOMAD)
 
 
 # EXCEPTIONS
@@ -66,15 +67,15 @@ def get_file_from_url(url, save_to, override=False):
         f.write(response.content)
 
 
-def download_lovd_database_for_eys_gene(override=False):
+def download_lovd_database_for_eys_gene(save_to=STORE_AS_LOVD, override=False):
     """
     Gets file from url and saves it into provided path. Overrides, if override is True.
 
+    :param str save_to: path to save (default: 'data/lovd/lovd_eys.txt')
     :param bool override: needs override
     """
 
     url = LOVD_FILE_URL_EYS
-    save_to = STORE_AS_LOVD
 
     # check if directory exists, if not - create
     save_to_dir = os.path.dirname(save_to)
@@ -176,19 +177,37 @@ def download_database_for_eys_gene(database_name, override=False):
     os.rename(latest_file, os_path)
 
 
-def store_database_for_eys_gene(database_name, override=False):
+def download_selected_database_for_eys_gene(database_name, save_path="", override=False):
     """
     Calls a function to download a database.
+
     :param database_name: the name of the database that should be downloaded
+    :param save_path: path to save the data
     :param override: should be already existing file be overwritten
     """
+    if not isinstance(database_name, str):
+        raise TypeError("Database name should be a string")
+
     database_name = database_name.lower()
+
+    # if save_path is not provided, save to default location
+    if database_name == "lovd" and save_path == "":
+        save_path = STORE_AS_LOVD
+    elif database_name == "gnomad" and save_path == "":
+        save_path = STORE_AS_GNOMAD
+
+    # check if database_name is supported
     if database_name not in DATABASES_DOWNLOAD_PATHS:
-        raise IndexError(f"Requested {database_name} database is not supported")
+        raise IndexError(f"Requested for {database_name} database is not supported")
+
+    # download the database
     if database_name == "lovd":
-        download_lovd_database_for_eys_gene(override)
+        download_lovd_database_for_eys_gene(save_path, override)
+    elif database_name == "gnomad":
+        download_data_from_gnomad_eys(save_path, override)
     else:
-        download_database_for_eys_gene(database_name, override)
+        raise IndexError(f"Requested for {database_name} is not yet supported")
+
 
 def prepare_popmax_calculation(df, pop_data, name, pop_ids, index):
     """
@@ -212,7 +231,7 @@ def prepare_popmax_calculation(df, pop_data, name, pop_ids, index):
             df.loc[index, f'{name}_an_{variant_id}'] = pop['an']
 
 
-def download_data_from_gnomad_eys(path, override=False):
+def download_data_from_gnomad_eys(path=STORE_AS_GNOMAD, override=False):
     """
     Requests gnomAD API for data about a specific gene containing:
     - variant_id
@@ -223,12 +242,15 @@ def download_data_from_gnomad_eys(path, override=False):
     - popmax
     - popmax population
 
-    :param str gene_name: name of gene
-    :param bool to_file: if True, saves data to variants.csv
-    :returns: DataFrame from gnomAD API
-    :rtype: DataFrame
+    :param str path: path to save the data (default: 'data/gnomad/gnomad_eys.csv')
+    :param bool override: should an existing file be overriden with a new one
     """
 
+    if os.path.exists(path) and not override:
+        print(f"The file at {path} already exists.")
+        logging.info("The file at %s already exists.", path)
+        return
+
     url = 'https://gnomad.broadinstitute.org/api'
     query = f"""
     query{{
@@ -276,9 +298,11 @@ def download_data_from_gnomad_eys(path, override=False):
         if not os.path.isfile(path):
             f = open('logs.txt', 'x')
             f.write(response.text)
+            logging.error("Error while downloading data from gnomAD API. Check logs.txt for more information.")
         else:
             f = open('logs.txt', 'a')
             f.write(response.text)
+            logging.error("Error while downloading data from gnomAD API. Check logs.txt for more information.")
 
     data = response.json()['data']['gene']['variants']
 
@@ -337,6 +361,4 @@ def download_data_from_gnomad_eys(path, override=False):
     df = df.filter(not_to_drop, axis="columns")
 
     if not os.path.isfile(path) or override:
-        df.to_csv(path, index=False)
-
-    return df
+        df.to_csv(path, index=False)

app/front-end/src/features/editor/components/editorView/editorConfirmLeave.tsx

@@ -0,0 +1,83 @@
+import { FileTreeItemContextMenuStyledDialog } from '@/features/editor/components/fileTreeView/fileTreeItem';
+import { useStatusContext } from '@/hooks';
+import { Close as CloseIcon } from '@mui/icons-material';
+import {
+  Box,
+  Button,
+  DialogActions,
+  DialogContent,
+  DialogTitle,
+  Grid,
+  IconButton,
+  Typography,
+  useTheme,
+} from '@mui/material';
+import { useCallback } from 'react';
+
+interface EditorConfirmLeaveDialogProps {
+  onConfirm: () => void;
+  isOpen: boolean;
+  onClose: () => void;
+}
+
+export const EditorConfirmLeave: React.FC<EditorConfirmLeaveDialogProps> = ({ onConfirm, isOpen, onClose }) => {
+  const { unsavedStateUpdate } = useStatusContext();
+  const Theme = useTheme();
+
+  const handleConfirm = useCallback(() => {
+    unsavedStateUpdate(false);
+    onConfirm();
+    onClose();
+  }, [onConfirm, onClose, unsavedStateUpdate]);
+
+  return (
+    <FileTreeItemContextMenuStyledDialog open={isOpen} onClose={onClose}>
+      <Grid container spacing={2} justifyContent='center' alignItems='center'>
+        <Grid item xs={8}>
+          <DialogTitle sx={{ color: Theme.palette.primary.main, pl: '1.5rem', pt: '1.5rem', fontWeight: '700' }}>
+            Unsaved changes
+          </DialogTitle>
+        </Grid>
+        <Grid item xs={4}>
+          <Box display='flex' justifyContent='flex-end'>
+            <IconButton
+              aria-label='close'
+              onClick={onClose}
+              sx={{
+                color: Theme.palette.primary.main,
+                mt: '0.5rem',
+                mr: '1.5rem',
+              }}
+            >
+              <CloseIcon />
+            </IconButton>
+          </Box>
+        </Grid>
+      </Grid>
+      <DialogContent sx={{ py: 0 }}>
+        <Typography sx={{ color: Theme.palette.text.primary, fontSize: '1rem', mb: '1rem' }}>
+          You have unsaved changes. If you continue, your <b>changes will be lost</b>. <br />
+          Do you wish to continue?
+        </Typography>
+      </DialogContent>
+      <DialogActions>
+        <Button onClick={onClose}>
+          <Typography sx={{ fontSize: '1rem', color: Theme.palette.text.secondary }}>Cancel</Typography>
+        </Button>
+        <Button
+          onClick={handleConfirm}
+          variant='outlined'
+          sx={{
+            borderColor: Theme.palette.primary.main,
+            ':hover': { borderColor: Theme.palette.primary.main, bgcolor: Theme.palette.secondary.main },
+            '& .MuiTouchRipple-root': {
+              color: Theme.palette.primary.main,
+            },
+          }}
+        >
+          Continue
+        </Button>
+      </DialogActions>
+    </FileTreeItemContextMenuStyledDialog>
+  );
+};

app/front-end/src/features/editor/components/editorView/editorToolbar.tsx

@@ -2,7 +2,7 @@ import { useStatusContext } from '@/hooks';
 import { socket } from '@/lib';
 import { Events } from '@/types';
 import { Done as DoneIcon, Error as ErrorIcon } from '@mui/icons-material';
-import { Box, Button, CircularProgress, useTheme } from '@mui/material';
+import { alpha, Box, Button, CircularProgress, Typography, useTheme } from '@mui/material';
 import {
   GridToolbarColumnsButton,
   GridToolbarContainer,
@@ -52,7 +52,7 @@ export const EditorToolbar: React.FC<EditorToolbarProps> = ({ handleSave }) => {
   const [saveStatus, setSaveStatus] = useState(true);
 
   const Theme = useTheme();
-  const { blocked } = useStatusContext();
+  const { blocked, unsavedStateUpdate, unsaved } = useStatusContext();
 
   useEffect(() => {
     const handleWorkspaceFileSaveFeedback = (data: { status: 'success' | 'error' }) => {
@@ -73,10 +73,17 @@ export const EditorToolbar: React.FC<EditorToolbarProps> = ({ handleSave }) => {
       <GridToolbarDensitySelector />
       {/* <GridToolbarExport /> */}
       <Box sx={{ flexGrow: 1 }} />
+      {unsaved && (
+        <Typography sx={{ fontSize: '0.9rem', color: alpha(Theme.palette.text.primary, 0.5), pr: '0.5rem' }}>
+          Changes not saved
+        </Typography>
+      )}
+
       <Button
         onClick={() => {
           setIsSaving(true);
           handleSave();
+          unsavedStateUpdate(false);
         }}
         disabled={blocked}
         startIcon={