Merge pull request #302 from pepkit/dev

Critical bug fixes
pepkit · Feb 26, 2024 · 367ae24 · 367ae24
2 parents 7a6a64c + fc3b1aa
commit 367ae24
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diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,7 +2,13 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.11.6] - 02-08-2024
+## [0.11.6] - 02-26-2024
+
+- Fix some bugs introduced as a result of the last release:
+  - tag's were being removed from the URL params when selecting a project view
+  - stabilized query params along the way on the namespace page
+
+## [0.11.7] - 02-22-2024
 
 - Added interface for selecting and viewing project views
 - optimized loading of very large sample tables

diff --git a/pephub/_version.py b/pephub/_version.py
@@ -1 +1 @@
-__version__ = "0.11.7"
+__version__ = "0.11.8"
diff --git a/pephub/dependencies.py b/pephub/dependencies.py
@@ -209,6 +209,38 @@ def get_project(
         )
 
 
+def get_config(
+    namespace: str,
+    project: str,
+    tag: Optional[str] = DEFAULT_TAG,
+    agent: PEPDatabaseAgent = Depends(get_db),
+) -> Dict[str, Any]:
+    try:
+        config = agent.project.get_config(namespace, project, tag)
+        yield config
+    except ProjectNotFoundError:
+        raise HTTPException(
+            404,
+            f"PEP '{namespace}/{project}:{tag or DEFAULT_TAG}' does not exist in database. Did you spell it correctly?",
+        )
+
+
+def get_subsamples(
+    namespace: str,
+    project: str,
+    tag: Optional[str] = DEFAULT_TAG,
+    agent: PEPDatabaseAgent = Depends(get_db),
+) -> Dict[str, Any]:
+    try:
+        subsamples = agent.project.get_subsamples(namespace, project, tag)
+        yield subsamples
+    except ProjectNotFoundError:
+        raise HTTPException(
+            404,
+            f"PEP '{namespace}/{project}:{tag or DEFAULT_TAG}' does not exist in database. Did you spell it correctly?",
+        )
+
+
 def get_project_annotation(
     namespace: str,
     project: str,

diff --git a/pephub/routers/api/v1/project.py b/pephub/routers/api/v1/project.py
@@ -44,6 +44,8 @@
 from ....dependencies import (
     get_db,
     get_project,
+    get_config,
+    get_subsamples,
     get_project_annotation,
     get_namespace_access_list,
     verify_user_can_fork,
@@ -413,29 +415,21 @@ async def get_pep_samples(
 
 @project.get("/config", summary="Get project configuration file")
 async def get_pep_config(
-    proj: Union[peppy.Project, dict] = Depends(get_project),
+    config: dict = Depends(get_config),
     format: Optional[Literal["JSON", "String"]] = "JSON",
-    raw: Optional[bool] = False,
 ):
     """
     Get project configuration file from a certain project and namespace
 
-    Don't have a namespace or project?
-
     Use the following:
 
         project: example
         namespace: databio
+        tag: default
     """
-    if raw:
-        proj_config = proj[CONFIG_KEY]
-    else:
-        proj_config = proj.to_dict(extended=True, orient="records")[CONFIG_KEY]
-    if format == "JSON":
-        return JSONResponse(proj_config)
     return JSONResponse(
         {
-            "config": yaml.dump(proj_config, sort_keys=False),
+            "config": yaml.dump(config, sort_keys=False),
         }
     )
 
@@ -622,8 +616,8 @@ async def delete_sample(
 
 
 @project.get("/subsamples")
-async def get_subsamples(
-    proj: peppy.Project = Depends(get_project),
+async def get_subsamples_endpoint(
+    subsamples: peppy.Project = Depends(get_subsamples),
     download: bool = False,
 ):
     """
@@ -636,16 +630,11 @@ async def get_subsamples(
         project: example
         namespace: databio
     """
-    if isinstance(proj, dict):
-        subsamples = proj[SUBSAMPLE_RAW_LIST_KEY]
-    else:
-        subsamples = proj.to_dict(extended=True, orient="records")[
-            SUBSAMPLE_RAW_LIST_KEY
-        ]
+
     if subsamples:
         try:
             subsamples = pd.DataFrame(
-                proj[SUBSAMPLE_RAW_LIST_KEY][0]
+                subsamples[0]
             )  # TODO: update this enpoint, so that it has access to all subsample tables
         except IndexError:
             subsamples = pd.DataFrame()
@@ -861,6 +850,7 @@ async def create_view_of_the_project(
     tag: str = DEFAULT_TAG,
     description: str = "",
     sample_names: List[str] = None,
+    no_fail: bool = False,
     namespace_access_list: List[str] = Depends(get_namespace_access_list),
     agent: PEPDatabaseAgent = Depends(get_db),
 ):
@@ -875,6 +865,7 @@ async def create_view_of_the_project(
     try:
         agent.view.create(
             view_name=view,
+            no_fail=no_fail,
             description=description,
             view_dict=CreateViewDictModel(
                 project_namespace=namespace,

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -1,7 +1,7 @@
 fastapi>=0.108.0
 psycopg>=3.1.15
-pepdbagent @ git+https://github.com/pepkit/pepdbagent.git@dev#egg=pepdbagent
-# pepdbagent>=0.7.3
+# pepdbagent @ git+https://github.com/pepkit/pepdbagent.git@dev#egg=pepdbagent
+pepdbagent>=0.8.0
 peppy>=0.40.1
 eido>=0.2.2
 jinja2>=3.1.2

diff --git a/web/src/components/namespace/search-bar.tsx b/web/src/components/namespace/search-bar.tsx
@@ -1,5 +1,6 @@
 import { FC } from 'react';
 import { set } from 'react-hook-form';
+import { useSearchParams } from 'react-router-dom';
 
 interface Props {
   namespace: string;
@@ -26,6 +27,7 @@ export const NamespacePageSearchBar: FC<Props> = ({
   setOrder,
   setOffset,
 }) => {
+  const [searchParams, setSearchParams] = useSearchParams();
   return (
     <div className="flex-row d-flex align-items-center" style={{ position: 'relative' }}>
       <div className="input-group shadow-sm">
@@ -37,6 +39,12 @@ export const NamespacePageSearchBar: FC<Props> = ({
           onChange={(e) => {
             setSearch(e.target.value);
             setOffset(0);
+            if (e.target.value === '') {
+              searchParams.delete('search');
+            } else {
+              searchParams.set('search', e.target.value);
+            }
+            setSearchParams(searchParams);
           }}
           id="search-bar"
           type="text"
@@ -47,9 +55,8 @@ export const NamespacePageSearchBar: FC<Props> = ({
           value={limit}
           onChange={(e) => {
             setLimit(parseInt(e.target.value));
-            const urlParams = new URLSearchParams(window.location.search);
-            urlParams.set('limit', e.target.value);
-            window.history.replaceState({}, '', `${window.location.pathname}?${urlParams}`);
+            searchParams.set('limit', e.target.value);
+            setSearchParams(searchParams);
           }}
           className="form-control form-select"
         >
@@ -64,10 +71,8 @@ export const NamespacePageSearchBar: FC<Props> = ({
             const [orderBy, order] = e.target.value.split('+');
             setOrderBy(orderBy);
             setOrder(order);
-            const urlParams = new URLSearchParams(window.location.search);
-            urlParams.set('orderBy', orderBy);
-            urlParams.set('order', order);
-            window.history.replaceState({}, '', `${window.location.pathname}?${urlParams}`);
+            searchParams.set('orderBy', orderBy);
+            setSearchParams(searchParams);
           }}
           className="form-control form-select"
         >

diff --git a/web/src/components/namespace/star-filter-bar.tsx b/web/src/components/namespace/star-filter-bar.tsx
@@ -1,11 +1,13 @@
 import { FC } from 'react';
+import { useSearchParams } from 'react-router-dom';
 
 interface Props {
   search: string;
   setSearch: (search: string) => void;
 }
 
 export const StarFilterBar: FC<Props> = ({ search, setSearch }) => {
+  const [searchParams, setSearchParams] = useSearchParams();
   return (
     <div className="flex-row d-flex align-items-center" style={{ position: 'relative' }}>
       <div className="input-group shadow-sm">
@@ -14,7 +16,15 @@ export const StarFilterBar: FC<Props> = ({ search, setSearch }) => {
         </span>
         <input
           value={search}
-          onChange={(e) => setSearch(e.target.value)}
+          onChange={(e) => {
+            setSearch(e.target.value);
+            if (e.target.value === '') {
+              searchParams.delete('search');
+            } else {
+              searchParams.set('search', e.target.value);
+            }
+            setSearchParams(searchParams);
+          }}
           id="search-bar"
           type="text"
           className="form-control w-60"

diff --git a/web/src/components/namespace/view-selector.tsx b/web/src/components/namespace/view-selector.tsx
@@ -1,6 +1,6 @@
 import { FC } from 'react';
 import Nav from 'react-bootstrap/Nav';
-import { NavLink } from 'react-router-dom';
+import { NavLink, useSearchParams } from 'react-router-dom';
 
 type View = 'peps' | 'pops' | 'stars';
 
@@ -14,7 +14,13 @@ type Props = {
 };
 
 export const NamespaceViewSelector: FC<Props> = (props) => {
+  const [searchParams, setSearchParams] = useSearchParams();
   const handleNavSelect = (eventKey: string | null) => {
+    if (eventKey === null) {
+      return;
+    }
+    searchParams.set('view', eventKey);
+    setSearchParams(searchParams);
     props.setView(eventKey as View);
   };
 

diff --git a/web/src/components/project/view-selector.tsx b/web/src/components/project/view-selector.tsx
@@ -5,6 +5,7 @@ import { useSearchParams } from 'react-router-dom';
 import ReactSelect from 'react-select';
 
 import { ProjectViewsResponse } from '../../api/project';
+import { search } from '../../api/search';
 
 interface Props {
   projectViewsIsLoading: boolean;
@@ -39,22 +40,15 @@ export const ViewSelector = (props: Props) => {
             })) || []
           }
           onChange={(selectedOption) => {
+            debugger;
             if (selectedOption === null) {
               setView(undefined);
               searchParams.delete('view');
-              setSearchParams(
-                new URLSearchParams({
-                  ...searchParams,
-                }),
-              );
+              setSearchParams(searchParams);
             } else {
               setView(selectedOption.value);
-              setSearchParams(
-                new URLSearchParams({
-                  ...searchParams,
-                  view: selectedOption.value,
-                }),
-              );
+              searchParams.set('view', selectedOption.value);
+              setSearchParams(searchParams);
             }
           }}
           isDisabled={projectViews?.views.length === 0 || projectViewsIsLoading}

diff --git a/web/src/pages/Namespace.tsx b/web/src/pages/Namespace.tsx
@@ -1,6 +1,6 @@
 import { FC, Fragment, useEffect, useState } from 'react';
 import Breadcrumb from 'react-bootstrap/Breadcrumb';
-import { useParams } from 'react-router-dom';
+import { useParams, useSearchParams } from 'react-router-dom';
 
 import { GitHubAvatar } from '../components/badges/github-avatar';
 import { PageLayout } from '../components/layout/page-layout';
@@ -24,9 +24,8 @@ import { numberWithCommas } from '../utils/etc';
 type View = 'peps' | 'pops' | 'stars';
 
 export const NamespacePage: FC = () => {
-  // get view out of url its a query param
-  const urlParams = new URLSearchParams(window.location.search);
-  const viewFromUrl = urlParams.get('view') as View;
+  const [searchParams, setSearchParams] = useSearchParams();
+  const viewFromUrl = searchParams.get('view') as View;
 
   // get namespace from url
   let { namespace } = useParams();
@@ -36,18 +35,18 @@ export const NamespacePage: FC = () => {
   const { user } = useSession();
 
   // pagination
-  const [limit, setLimit] = useState(urlParams.get('limit') ? parseInt(urlParams.get('limit')!) : 10);
-  const [offset, setOffset] = useState(urlParams.get('offset') ? parseInt(urlParams.get('offset')!) : 0);
-  const [search, setSearch] = useState(urlParams.get('search') || '');
-  const [orderBy, setOrderBy] = useState(urlParams.get('orderBy') || 'update_date');
-  const [order, setOrder] = useState(urlParams.get('order') || 'asc');
+  const [limit, setLimit] = useState(searchParams.get('limit') ? parseInt(searchParams.get('limit')!) : 10);
+  const [offset, setOffset] = useState(searchParams.get('offset') ? parseInt(searchParams.get('offset')!) : 0);
+  const [search, setSearch] = useState(searchParams.get('search') || '');
+  const [orderBy, setOrderBy] = useState(searchParams.get('orderBy') || 'update_date');
+  const [order, setOrder] = useState(searchParams.get('order') || 'asc');
 
   // state
   const [showAddPEPModal, setShowAddPEPModal] = useState(false);
   const [showEndpointsModal, setShowEndpointsModal] = useState(false);
   const [showGeoDownloadModal, setShowGeoDownloadModal] = useState(false);
   const [view, setView] = useState<View>(viewFromUrl === 'stars' ? 'stars' : 'peps');
-  const [starSearch, setStarSearch] = useState<string>(urlParams.get('starSearch') || '');
+  const [starSearch, setStarSearch] = useState<string>(searchParams.get('starSearch') || '');
 
   const searchDebounced = useDebounce<string>(search, 500);
 
@@ -75,31 +74,6 @@ export const NamespacePage: FC = () => {
   // left over from when we were filtering on sample number
   const projectsFiltered = projects?.items.filter((p) => p.number_of_samples) || [];
 
-  // update url when search changes
-  useEffect(() => {
-    if (typeof window !== 'undefined' && search === '') {
-      const urlParams = new URLSearchParams(window.location.search);
-      urlParams.delete('search');
-      window.history.replaceState({}, '', `${window.location.pathname}?${urlParams}`);
-    } else if (typeof window !== 'undefined') {
-      const urlParams = new URLSearchParams(window.location.search);
-      urlParams.set('search', search);
-      window.history.replaceState({}, '', `${window.location.pathname}?${urlParams}`);
-    }
-  }, [search]);
-
-  useEffect(() => {
-    if (typeof window !== 'undefined' && starSearch === '') {
-      const urlParams = new URLSearchParams(window.location.search);
-      urlParams.delete('starSearch');
-      window.history.replaceState({}, '', `${window.location.pathname}?${urlParams}`);
-    } else if (typeof window !== 'undefined') {
-      const urlParams = new URLSearchParams(window.location.search);
-      urlParams.set('starSearch', starSearch);
-      window.history.replaceState({}, '', `${window.location.pathname}?${urlParams}`);
-    }
-  }, [starSearch]);
-
   if (namespaceInfoIsLoading || starsIsLoading) {
     return (
       <PageLayout title={namespace}>