From 46f1c6fa6eec1fc67bc5f1faad6ec556b8b3a0c5 Mon Sep 17 00:00:00 2001
From: fnguyen <OrdinaryNeumann@gmail.com>
Date: Wed, 13 Nov 2024 16:16:03 -0500
Subject: [PATCH] Remove deprecated HTSGetBrowser

---
 src/store/api.js                        |  23 ----
 src/views/genomicsData/HtsgetBrowser.js | 142 ------------------------
 2 files changed, 165 deletions(-)
 delete mode 100644 src/views/genomicsData/HtsgetBrowser.js

diff --git a/src/store/api.js b/src/store/api.js
index c5230145..d98eed14 100644
--- a/src/store/api.js
+++ b/src/store/api.js
@@ -16,29 +16,6 @@ export function fetchOrRelogin(...args) {
     });
 }
 
-// API Calls
-/* 
-Fetch katsu calls
-*/
-export function fetchKatsu(URL) {
-    // This code is no longer used, however we have decided to archive the HTSGetBrowser class
-    // which depends on this. Therefore, this is kept for posterity
-    /*
-    return fetch(`${katsu}/moh/v1/discovery/overview/${URL}`)
-        .then((response) => {
-            if (response.ok) {
-                return response.json();
-            }
-            console.log(`Katsu: ${response}`);
-            throw new Error(`Katsu: ${response}`);
-        })
-        .catch((error) => {
-            console.log(`Error: ${error}`);
-            return 'error';
-        });
-    */
-}
-
 export function fetchFederationStat(endpoint) {
     return fetchOrRelogin(`${federation}/fanout`, {
         method: 'post',
diff --git a/src/views/genomicsData/HtsgetBrowser.js b/src/views/genomicsData/HtsgetBrowser.js
deleted file mode 100644
index 2f0048d7..00000000
--- a/src/views/genomicsData/HtsgetBrowser.js
+++ /dev/null
@@ -1,142 +0,0 @@
-import { useState, useEffect } from 'react';
-import { Box, Button, FormControl, Grid } from '@mui/material';
-import MainCard from 'ui-component/cards/MainCard';
-
-import { MultiSelect } from 'react-multi-select-component';
-import LightCard from 'views/dashboard/Default/LightCard';
-import AlertComponent from 'ui-component/AlertComponent';
-
-import HtsgetInstance from 'ui-component/IGV/HtsgetInstance';
-import { fetchKatsu } from 'store/api';
-
-import { LoadingIndicator, usePromiseTracker, trackPromise } from 'ui-component/LoadingIndicator/LoadingIndicator';
-
-// Assets
-import MapIcon from '@mui/icons-material/Map';
-import DescriptionIcon from '@mui/icons-material/Description';
-
-import 'assets/css/VariantsSearch.css';
-
-function HtsgetBrowser() {
-    const [isLoading, setLoading] = useState(true);
-    // const events = useSelector((state) => state);
-    const [BamCount, setBamCount] = useState('');
-    const [VcfCount, setVcfCount] = useState('');
-    const { promiseInProgress } = usePromiseTracker();
-    const options = useState([]);
-    const [selected, setSelected] = useState([]);
-    const [open, setOpen] = useState(false);
-    const [selectedBamIds, setSelectedBamIds] = useState([]);
-    const [selectedVcfIds, setSelectedVcfIds] = useState([]);
-    const [alertMessage, _setAlertMessage] = useState('');
-    const [alertSeverity, _setAlertSeverity] = useState('');
-
-    useEffect(() => {
-        setSelected([]);
-        options.length = 0;
-        setSelectedBamIds([]);
-        setSelectedVcfIds([]);
-        setLoading(false);
-
-        // Get a list of genomics files available
-        trackPromise(
-            fetchKatsu('/api/genomicsreports')
-                .then((_data) => {
-                    // TODO: get a list of ids of genomics files from API above
-                    // Or any other APIs that can provide a list of IDs
-                    // Note: if only VCF files are served, then the following TODOs concerning BAM files
-                    // can all be removed.
-                })
-                .catch(() => {
-                    setBamCount('Not Available');
-                    setVcfCount('Not Available');
-                })
-        );
-    }, [options]);
-
-    const formHandler = (e) => {
-        e.preventDefault(); // Prevent form submission
-
-        // TODO: Dynamically create a list of IDs that have been selected
-        // TODO: And pass this list of IDs into htsgetInstance
-        setSelectedBamIds([]);
-        setSelectedVcfIds([]);
-    };
-
-    return (
-        <MainCard title="Htsget Browser" sx={{ minHeight: 830, position: 'relative' }}>
-            <AlertComponent
-                open={open}
-                setOpen={setOpen}
-                text={alertMessage}
-                severity={alertSeverity}
-                variant="filled"
-                fontColor={alertSeverity === 'error' ? 'white' : 'black'}
-            />
-            <Grid container direction="column" className="content">
-                <Grid container direction="row" justifyContent="center" spacing={2} p={2}>
-                    <Grid item sm={12} xs={12} md={4} lg={4}>
-                        {promiseInProgress === true ? (
-                            <LoadingIndicator />
-                        ) : (
-                            <LightCard
-                                isLoading={isLoading}
-                                header="VCFs"
-                                value={VcfCount}
-                                icon={<MapIcon fontSize="inherit" />}
-                                color="primary"
-                            />
-                        )}
-                    </Grid>
-                    <Grid item sm={12} xs={12} md={4} lg={4}>
-                        {promiseInProgress === true ? (
-                            <LoadingIndicator />
-                        ) : (
-                            <LightCard
-                                isLoading={isLoading}
-                                header="BAMs"
-                                value={BamCount}
-                                icon={<DescriptionIcon fontSize="inherit" />}
-                                color="secondary"
-                            />
-                        )}
-                    </Grid>
-                </Grid>
-
-                <form onSubmit={formHandler} style={{ justifyContent: 'center' }}>
-                    <Grid container direction="row" justifyContent="center" alignItems="center" spacing={2} p={2}>
-                        <Grid item>
-                            {options.length > 0 && (
-                                <FormControl>
-                                    <Grid container direction="row" alignItems="center">
-                                        <Box mr={2}>
-                                            <p>Genomics Files</p>
-                                        </Box>
-                                        <MultiSelect // Width set in CSS
-                                            options={options}
-                                            value={selected}
-                                            onChange={setSelected}
-                                            labelledBy="Genomics Files"
-                                        />
-                                    </Grid>
-                                </FormControl>
-                            )}
-                        </Grid>
-
-                        <Grid item>
-                            <FormControl>
-                                <Button type="submit" variant="contained">
-                                    View
-                                </Button>
-                            </FormControl>
-                        </Grid>
-                    </Grid>
-                </form>
-
-                <HtsgetInstance BamIdList={selectedBamIds} VcfIdList={selectedVcfIds} />
-            </Grid>
-        </MainCard>
-    );
-}
-
-export default HtsgetBrowser;