Dev aaron

pephub/routers/api/v1/project.py

@@ -98,7 +98,7 @@ async def update_a_pep(
     if namespace not in (list_of_admins or []):
         return JSONResponse(
             content={
-                "message": "Unothorized for updating projects.",
+                "message": "Unauthorized for updating projects.",
             },
             status_code=401,
         )
@@ -109,24 +109,12 @@ async def update_a_pep(
 
     # sample table update
     if updated_project.sample_table is not None:
-        sample_table_df = pd.DataFrame.from_dict(updated_project.sample_table)
-        sample_table_df_json = sample_table_df.to_dict(orient="records")
-
-        new_raw_project[SAMPLE_RAW_DICT_KEY] = sample_table_df_json
+        new_raw_project[SAMPLE_RAW_DICT_KEY] = updated_project.sample_table
         new_raw_project[CONFIG_KEY] = current_project.config.to_dict()
 
     # subsample table update
-    if updated_project.subsample_table is not None:
-        subsample_peppy_list = []
-        for subsample in updated_project.subsample_table:
-            subsample_str = subsample.rstrip(",")
-            subsample_str = StringIO(subsample_str)
-            subsample_pd = pd.read_csv(subsample_str)
-            subsample_df = subsample_pd.to_dict(orient="records")
-
-            subsample_peppy_list.append(subsample_df)
-
-        new_raw_project[SUBSAMPLE_RAW_LIST_KEY] = subsample_peppy_list
+    if updated_project.subsample_tables is not None:
+        new_raw_project[SUBSAMPLE_RAW_LIST_KEY] = updated_project.subsample_tables
 
     if updated_project.description:
         new_raw_project["_config"]["description"] = updated_project.description
@@ -141,7 +129,7 @@ async def update_a_pep(
         [
             updated_project.project_config_yaml is not None,
             updated_project.sample_table is not None,
-            updated_project.subsample_table is not None,
+            updated_project.subsample_tables is not None,
         ]
     ):
         try:
@@ -151,20 +139,17 @@ async def update_a_pep(
                 status_code=400,
                 detail=f"Could not create PEP from provided yaml. Error: {e}",
             )
-        # validate each sample in the table according to the project
-        for s in new_project.samples:
-            sample_name: str = s[new_project.st_index]
-            try:
-                eido.validate_sample(
-                    new_project,
-                    sample_name,
-                    "http://schema.databio.org/pep/2.0.0.yaml",  # just use the base PEP schema for now
-                )
-            except Exception as e:
-                raise HTTPException(
-                    status_code=400,
-                    detail=f"Sample {sample_name} failed validation: {e}",
-                )
+
+        try:
+            # validate project (it will also validate samples)
+            eido.validate_project(
+                new_project, "http://schema.databio.org/pep/2.1.0.yaml"
+            )
+        except Exception as e:
+            raise HTTPException(
+                status_code=400,
+                detail=f"",
+            )
 
         # if we get through all samples, then update project in the database
         agent.project.update(

pephub/routers/models.py

@@ -11,7 +11,7 @@ class ProjectOptional(UpdateItems):
     sample_table: Optional[List[dict]]
     project_config_yaml: Optional[str]
     description: Optional[str]
-    subsample_table: Optional[List[dict]]
+    subsample_tables: Optional[List[List[dict]]]
 
     class Config:
         allow_population_by_field_name = True

web/src/api/project.ts

@@ -194,3 +194,29 @@ export const editProjectSubsampleTable = (
     { headers: { Authorization: `Bearer ${token}` } },
   );
 };
+
+export const editTotalProject = (
+  namespace: string,
+  projectName: string,
+  tag: string = 'default',
+  token: string | null,
+  data: {
+    config?: string;
+    samples?: Sample[];
+    subsamples?: Sample[];
+  },
+) => {
+  const url = `${API_BASE}/projects/${namespace}/${projectName}?tag=${tag}`;
+  let requestBody = {};
+  if (data.config) {
+    requestBody = { ...requestBody, project_config_yaml: data.config };
+  }
+  if (data.samples) {
+    requestBody = { ...requestBody, sample_table: data.samples };
+  }
+  if (data.subsamples && data.subsamples.length > 0) {
+    requestBody = { ...requestBody, subsample_tables: [data.subsamples] };
+  }
+
+  return axios.patch(url, requestBody, { headers: { Authorization: `Bearer ${token}` } });
+};

web/src/components/layout/nav.tsx

@@ -182,11 +182,11 @@ export const Nav: FC = () => {
                 <i className="bi bi-check2-circle me-1"></i>Validation
               </a>
             </li>
-            <li className="text-body mx-2 my-0 nav-item h5 pt-1">
-              <a className="nav-link" href="/about">
-                <i className="bi bi-info-circle me-1"></i>About
-              </a>
-            </li>
+            {/*<li className="text-body mx-2 my-0 nav-item h5 pt-1">*/}
+            {/*  <a className="nav-link" href="/about">*/}
+            {/*    <i className="bi bi-info-circle me-1"></i>About*/}
+            {/*  </a>*/}
+            {/*</li>*/}
             <li className="text-body mx-2 my-0 nav-item h5 pt-1">
               {user ? (
                 <div className="mx-2 my-0 nav-item h5 pt-1">

web/src/components/markdown/render.tsx

@@ -1,4 +1,4 @@
-import { FC } from 'react';
+import { FC, useEffect, useState } from 'react';
 import { ReactMarkdown } from 'react-markdown/lib/react-markdown';
 import remarkBreaks from 'remark-breaks';
 import remarkGfm from 'remark-gfm';

web/src/hooks/mutations/useTotalProjectChangeMutation.ts

@@ -0,0 +1,35 @@
+import { useMutation, useQueryClient } from '@tanstack/react-query';
+import { AxiosError } from 'axios';
+import { toast } from 'react-hot-toast';
+
+import { Sample } from '../../../types';
+import { editTotalProject } from '../../api/project';
+
+interface TotalProjectChangeMutationProps {
+  config?: string;
+  samples?: Sample[];
+  subsamples?: Sample[];
+}
+
+export const useTotalProjectChangeMutation = (
+  namespace: string,
+  project: string,
+  tag: string,
+  jwt: string,
+  data: TotalProjectChangeMutationProps,
+) => {
+  const queryClient = useQueryClient();
+
+  const mutation = useMutation({
+    mutationFn: () => editTotalProject(namespace || '', project || '', tag, jwt || '', data),
+    onSuccess: () => {
+      queryClient.invalidateQueries([namespace, project, tag]);
+      toast.success('Successfully updated the project!');
+    },
+    onError: (error: AxiosError) => {
+      toast.error(`Failed to update project: ${error}`);
+    },
+  });
+
+  return mutation;
+};

web/src/pages/About.tsx

@@ -10,8 +10,8 @@ function About() {
     <PageLayout fullWidth>
       <div className="mx-5" style={{ height: '80vh' }}>
         <div className="d-flex flex-column align-items-center justify-content-center">
-          <div className="row align-items-center">
-            <h1 className="fw-bolder">Let's build from here.</h1>
+          <div className="row align-items-center mt-2">
+            <h1 className="fw-bolder">Coming soon.</h1>
           </div>
         </div>
       </div>

web/src/pages/Project.tsx

@@ -19,6 +19,7 @@ import { SampleTable } from '../components/tables/sample-table';
 import { useConfigMutation } from '../hooks/mutations/useConfigMutation';
 import { useSampleTableMutation } from '../hooks/mutations/useSampleTableMutation';
 import { useSubsampleTableMutation } from '../hooks/mutations/useSubsampleTableMutation';
+import { useTotalProjectChangeMutation } from '../hooks/mutations/useTotalProjectChangeMutation';
 import { useProject } from '../hooks/queries/useProject';
 import { useProjectConfig } from '../hooks/queries/useProjectConfig';
 import { useSampleTable } from '../hooks/queries/useSampleTable';
@@ -137,19 +138,29 @@ export const ProjectPage: FC = () => {
     jwt || '',
     newProjectSubsamples,
   );
+  const totalProjectMutation = useTotalProjectChangeMutation(namespace || '', project || '', tag, jwt || '', {
+    config: newProjectConfig,
+    samples: newProjectSamples,
+    subsamples: newProjectSubsamples,
+  });
+
+  const handleTotalProjectChange = async () => {
+    await totalProjectMutation.mutateAsync();
+    runValidation();
+  };
 
   const handleProjectChange = async () => {
     if (configIsDirty) {
       await configMutation.mutateAsync();
-      runValidation(); 
+      runValidation();
     }
     if (samplesIsDirty) {
       await sampleTableMutation.mutateAsync();
-      runValidation(); 
+      runValidation();
     }
     if (subsamplesIsDirty) {
       await subsampleTableMutation.mutateAsync();
-      runValidation(); 
+      runValidation();
     }
   };
 
@@ -185,9 +196,9 @@ export const ProjectPage: FC = () => {
             ) : null}
           </Breadcrumb>
           <div className="ms-2 mb-1">
-          <a className="text-decoration-none" href={`https://schema.databio.org/${projectInfo?.pep_schema}.yaml`}>
-            <SchemaTag schema={projectInfo?.pep_schema} />
-          </a>
+            <a className="text-decoration-none" href={`https://schema.databio.org/${projectInfo?.pep_schema}.yaml`}>
+              <SchemaTag schema={projectInfo?.pep_schema} />
+            </a>
           </div>
         </div>
         <div className="d-flex flex-row align-items-start btn-g">
@@ -321,7 +332,7 @@ export const ProjectPage: FC = () => {
                           subsampleTableMutation.isLoading ||
                           !(configIsDirty || samplesIsDirty || subsamplesIsDirty)
                         }
-                        onClick={() => handleProjectChange()}
+                        onClick={() => handleTotalProjectChange()}
                         className="fst-italic btn btn-sm btn-success me-1 mb-1 border-dark"
                       >
                         {configMutation.isLoading || sampleTableMutation.isLoading || subsampleTableMutation.isLoading
@@ -369,17 +380,19 @@ export const ProjectPage: FC = () => {
                 />
               </>
             ) : (
-              <ProjectConfigEditor
-                readOnly={!(projectInfo && canEdit(user, projectInfo))}
-                value={
-                  projectConfigIsLoading
-                    ? 'Loading.'
-                    : projectConfig?.config
-                    ? newProjectConfig
-                    : 'No config file found.'
-                }
-                setValue={(value) => setNewProjectConfig(value)}
-              />
+              <div className="border border-t">
+                <ProjectConfigEditor
+                  readOnly={!(projectInfo && canEdit(user, projectInfo))}
+                  value={
+                    projectConfigIsLoading
+                      ? 'Loading.'
+                      : projectConfig?.config
+                      ? newProjectConfig
+                      : 'No config file found.'
+                  }
+                  setValue={(value) => setNewProjectConfig(value)}
+                />
+              </div>
             )}
           </div>
         </div>