diff --git a/api/__init__.py b/api/__init__.py index b407f4e..8de60d4 100644 --- a/api/__init__.py +++ b/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 diff --git a/api/data/__init__.py b/api/data/__init__.py index a2a2249..b2bc9c1 100644 --- a/api/data/__init__.py +++ b/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 diff --git a/api/data/constants.py b/api/data/constants.py index bf8e942..69e76d1 100644 --- a/api/data/constants.py +++ b/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" diff --git a/api/data/downloading.py b/api/data/downloading.py index 0d43d40..c253f14 100644 --- a/api/data/downloading.py +++ b/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 \ No newline at end of file + df.to_csv(path, index=False) \ No newline at end of file diff --git a/app/front-end/src/features/editor/components/editorView/editorConfirmLeave.tsx b/app/front-end/src/features/editor/components/editorView/editorConfirmLeave.tsx new file mode 100644 index 0000000..a128ef5 --- /dev/null +++ b/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 = ({ onConfirm, isOpen, onClose }) => { + const { unsavedStateUpdate } = useStatusContext(); + const Theme = useTheme(); + + const handleConfirm = useCallback(() => { + unsavedStateUpdate(false); + onConfirm(); + onClose(); + }, [onConfirm, onClose, unsavedStateUpdate]); + + return ( + + + + + Unsaved changes + + + + + + + + + + + + + You have unsaved changes. If you continue, your changes will be lost.
+ Do you wish to continue? + + + + + + + + ); +}; diff --git a/app/front-end/src/features/editor/components/editorView/editorToolbar.tsx b/app/front-end/src/features/editor/components/editorView/editorToolbar.tsx index ad2eb32..da684c0 100644 --- a/app/front-end/src/features/editor/components/editorView/editorToolbar.tsx +++ b/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 = ({ 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 = ({ handleSave }) => { {/* */} + {unsaved && ( + + Changes not saved + + )} +