Merge branch 'master' into dependabot/npm_and_yarn/compose/neurosynth…

…-frontend/multi-81f6ed4da7
neurostuff · Jan 6, 2025 · 21cc012 · 21cc012
2 parents faa0632 + a6b7c8c
commit 21cc012
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diff --git a/.github/workflows/deploy-to-staging.yml b/.github/workflows/deploy-to-staging.yml
@@ -70,8 +70,8 @@ jobs:
           # Wait for PostgreSQL to be ready
           until docker compose exec store_pgsql pg_isready; do sleep 5; done
 
-          docker compose exec store flask db migrate
-          docker compose exec store flask db upgrade
+          docker compose exec neurostore flask db migrate
+          docker compose exec neurostore flask db upgrade
         '
 
     - name: Run Docker commands in compose directory if changes detected

diff --git a/compose/neurosynth-frontend/src/App.tsx b/compose/neurosynth-frontend/src/App.tsx
@@ -1,82 +1,79 @@
-import Close from "@mui/icons-material/Close";
-import { IconButton } from "@mui/material";
-import { AxiosError } from "axios";
-import useGoogleAnalytics from "hooks/useGoogleAnalytics";
-import { SnackbarKey, SnackbarProvider } from "notistack";
-import { useEffect, useRef } from "react";
-import { QueryCache, QueryClient, QueryClientProvider } from "react-query";
-import Navbar from "components/Navbar/Navbar";
-import useGetToken from "./hooks/useGetToken";
-import BaseNavigation from "pages/BaseNavigation/BaseNavigation";
-import { useLocation } from "react-router-dom";
-import Downbanner from "components/Downbanner";
+import Close from '@mui/icons-material/Close';
+import { IconButton } from '@mui/material';
+import { AxiosError } from 'axios';
+import useGoogleAnalytics from 'hooks/useGoogleAnalytics';
+import { SnackbarKey, SnackbarProvider } from 'notistack';
+import { useEffect, useRef } from 'react';
+import { QueryCache, QueryClient, QueryClientProvider } from 'react-query';
+import Navbar from 'components/Navbar/Navbar';
+import useGetToken from './hooks/useGetToken';
+import BaseNavigation from 'pages/BaseNavigation/BaseNavigation';
+import { useLocation } from 'react-router-dom';
 
 const queryClient = new QueryClient({
-  defaultOptions: {
-    queries: {
-      retry: 0,
-      refetchOnWindowFocus: false,
-      // staleTime: 5000, // https://tkdodo.eu/blog/practical-react-query#the-defaults-explained
+    defaultOptions: {
+        queries: {
+            retry: 0,
+            refetchOnWindowFocus: false,
+            // staleTime: 5000, // https://tkdodo.eu/blog/practical-react-query#the-defaults-explained
+        },
     },
-  },
-  queryCache: new QueryCache({
-    onError: (error) => {
-      console.log({ error });
-      const responseStatus = (error as AxiosError)?.response?.status;
-      if (responseStatus && responseStatus === 404) {
-        console.error("could not find resource");
-      }
-    },
-  }),
+    queryCache: new QueryCache({
+        onError: (error) => {
+            console.log({ error });
+            const responseStatus = (error as AxiosError)?.response?.status;
+            if (responseStatus && responseStatus === 404) {
+                console.error('could not find resource');
+            }
+        },
+    }),
 });
 
 declare global {
-  interface Window {
-    gtag?: (
-      type: "event" | "config" | "get" | "set" | "consent",
-      action: "login" | "page_view",
-      options?: any
-    ) => void;
-  }
+    interface Window {
+        gtag?: (
+            type: 'event' | 'config' | 'get' | 'set' | 'consent',
+            action: 'login' | 'page_view',
+            options?: any
+        ) => void;
+    }
 }
 
 function App() {
-  const notistackRef = useRef<SnackbarProvider>(null);
-  useGetToken();
-  useGoogleAnalytics();
+    const notistackRef = useRef<SnackbarProvider>(null);
+    useGetToken();
+    useGoogleAnalytics();
 
-  const location = useLocation();
-  useEffect(() => {
-    if (window.gtag) {
-      window.gtag("event", "page_view", {
-        page_path: `${location.pathname}${location.search}`,
-      });
-    }
-  }, [location]);
+    const location = useLocation();
+    useEffect(() => {
+        if (window.gtag) {
+            window.gtag('event', 'page_view', {
+                page_path: `${location.pathname}${location.search}`,
+            });
+        }
+    }, [location]);
 
-  const handleCloseSnackbar =
-    (key: SnackbarKey) => (_event: React.MouseEvent) => {
-      if (notistackRef?.current?.closeSnackbar)
-        notistackRef.current?.closeSnackbar(key);
+    const handleCloseSnackbar = (key: SnackbarKey) => (_event: React.MouseEvent) => {
+        if (notistackRef?.current?.closeSnackbar) notistackRef.current?.closeSnackbar(key);
     };
 
-  return (
-    <QueryClientProvider client={queryClient}>
-      <SnackbarProvider
-        ref={notistackRef}
-        autoHideDuration={8000}
-        action={(key) => (
-          <IconButton onClick={handleCloseSnackbar(key)}>
-            <Close sx={{ color: "white" }} />
-          </IconButton>
-        )}
-      >
-        <Downbanner />
-        <Navbar />
-        <BaseNavigation />
-      </SnackbarProvider>
-    </QueryClientProvider>
-  );
+    return (
+        <QueryClientProvider client={queryClient}>
+            <SnackbarProvider
+                ref={notistackRef}
+                autoHideDuration={8000}
+                action={(key) => (
+                    <IconButton onClick={handleCloseSnackbar(key)}>
+                        <Close sx={{ color: 'white' }} />
+                    </IconButton>
+                )}
+            >
+                {/* <Banner /> */}
+                <Navbar />
+                <BaseNavigation />
+            </SnackbarProvider>
+        </QueryClientProvider>
+    );
 }
 
 export default App;
diff --git a/compose/neurosynth-frontend/src/components/Banner.tsx b/compose/neurosynth-frontend/src/components/Banner.tsx
@@ -0,0 +1,64 @@
+import { Cancel } from '@mui/icons-material';
+import EmojiPeopleIcon from '@mui/icons-material/EmojiPeople';
+import { Box, IconButton, Link } from '@mui/material';
+import BaseNavigationStyles from 'pages/BaseNavigation/BaseNavigation.styles';
+import { useState } from 'react';
+
+const localStorageBannerKey = 'hide-banner-nov-20-2024';
+
+const Banner: React.FC = () => {
+    const shouldHide = !!localStorage.getItem(localStorageBannerKey);
+    const [hideBanner, setHideBanner] = useState(shouldHide);
+
+    if (hideBanner) return <></>;
+
+    return (
+        <Box
+            sx={{
+                backgroundColor: 'primary.dark',
+                color: 'primary.contrastText',
+                width: '100%',
+                paddingY: '0.5rem',
+            }}
+        >
+            <Box
+                sx={[
+                    BaseNavigationStyles.pagesContainer,
+                    {
+                        marginY: '0',
+                        display: 'flex',
+                        alignItems: 'center',
+                        justifyContent: 'space-between',
+                    },
+                ]}
+            >
+                <Box display="flex" alignItems="center">
+                    <EmojiPeopleIcon sx={{ mr: '1rem' }} />
+                    Join us next Wednesday, December 4th 2024 at 10:00 ET for the Neurosynth Compose Virtual Town Hall!{' '}
+                    <Link
+                        color="primary.contrastText"
+                        sx={{ marginLeft: '4px' }}
+                        href="https://tally.so/r/nWePVR"
+                        target="_blank"
+                    >
+                        Click here to register
+                    </Link>
+                </Box>
+                <IconButton
+                    onClick={() => {
+                        localStorage.setItem(localStorageBannerKey, 'true');
+                        setHideBanner(true);
+                    }}
+                    sx={{
+                        padding: 0,
+                        ':hover': { backgroundColor: 'gray' },
+                    }}
+                >
+                    <Cancel />
+                </IconButton>
+            </Box>
+        </Box>
+    );
+};
+
+export default Banner;
diff --git a/compose/neurosynth-frontend/src/components/Downbanner.tsx b/compose/neurosynth-frontend/src/components/Downbanner.tsx
diff --git a/store/neurostore/resources/base.py b/store/neurostore/resources/base.py
@@ -8,6 +8,8 @@
 from flask import abort, request, current_app  # jsonify
 from flask.views import MethodView
 
+from psycopg2 import errors
+
 import sqlalchemy as sa
 import sqlalchemy.sql.expression as sae
 from sqlalchemy.orm import (
@@ -21,7 +23,7 @@
 
 from ..core import cache
 from ..database import db
-from .utils import get_current_user
+from .utils import get_current_user, validate_search_query, pubmed_to_tsquery
 from ..models import (
     StudysetStudy,
     AnnotationAnalysis,
@@ -613,7 +615,11 @@ def search(self):
         if s is not None and s.isdigit():
             q = q.filter_by(pmid=s)
         elif s is not None and self._fulltext_fields:
-            tsquery = sa.func.websearch_to_tsquery("english", s)
+            try:
+                validate_search_query(s)
+            except errors.SyntaxError as e:
+                abort(400, description=e.args[0])
+            tsquery = func.to_tsquery('english', pubmed_to_tsquery(s))
             q = q.filter(m._ts_vector.op("@@")(tsquery))
 
         # Alternatively (or in addition), search on individual fields.