added new object submission page

client/src/components/Admin/AddNewObject.js

@@ -1,34 +1,92 @@
 import React, { useState, useEffect } from 'react';
 import axios from 'axios';
 import styled from 'styled-components';
-import CustomMessages from '../Shared/CustomMessages';
 import CustomSelect from '../Shared/CustomSelect';
 import CustomInputText from '../Shared/CustomInputText';
-import { InputTextarea } from 'primereact/inputtextarea';
 import {dataTypes} from '../Shared/Enums';
+import datasetNoteObj from './JSONStructures/datasetnote';
+import { psetDataset, genericDataset, clinicalDataset } from './JSONStructures/dataset';
+import { baseDataObject, genomeDataObject } from './JSONStructures/dataobject';
+import ObjectTextArea from './SubComponents/ObjectTextArea';
 
 const StyledAddNewObject = styled.div`
   width: 800px;
+  .dropdown {
+    margin-bottom: 10px;
+  }
+
 `;
 
 const AddNewObject = () => {
 
   const [selected, setSelected] = useState(null);
   const [datasetName, setDatasetName] = useState('');
-  const [datasetNote, setDatasetNote] = useState('');
-  const [dataset, setDataset] = useState('');
-  const [dataObj, setDataObj] = useState('');
+  const [datasetNote, setDatasetNote] = useState({text: '', submitting: false, id: ''});
+  const [dataset, setDataset] = useState({text: '', submitting: false, id: ''});
+  const [dataObj, setDataObj] = useState({text: '', submitting: false, id: ''});
 
   useEffect(() => {
     if(selected){
+      setDatasetNote({...datasetNote, text: JSON.stringify(datasetNoteObj, null, 2)});
+      if(selected.value === 'pset'){
+        setDataset({...dataset, text: JSON.stringify(psetDataset, null, 2)});
+      }else if(selected.value === 'clinicalgenomics' || selected.value === 'clinical_icb'){
+        setDataset({...dataset, text: JSON.stringify(clinicalDataset, null, 2)});
+      }else{
+        setDataset({...dataset, text: JSON.stringify(genericDataset, null, 2)});
+      }
+      if(selected.value === 'pset' || selected.value === 'radioset'){
+        setDataObj({...dataObj, text: JSON.stringify(genomeDataObject, null, 2)});
+      }else{
+        setDataObj({...dataObj, text: JSON.stringify(baseDataObject, null, 2)});
+      }
+    }
+  }, [selected]);
 
+  useEffect(() => {
+    if(selected){
+      let noteObj = JSON.parse(datasetNote.text);
+      let datasetObj = JSON.parse(dataset.text);
+      let dataObject = JSON.parse(dataObj.text);
+      noteObj.name = datasetName;
+      datasetObj.name = datasetName;
+      dataObject.name = datasetName;
+      setDatasetNote({...datasetNote, text: JSON.stringify(noteObj, null, 2)});
+      setDataset({...dataset, text: JSON.stringify(datasetObj, null, 2)});
+      setDataObj({...dataObj, text: JSON.stringify(dataObject, null, 2)});
     }
-  }, [selected])
+  }, [datasetName]);
+
+  const submitObject = (type, object) => async (e) => {
+    e.preventDefault();
+    try{
+      const res = await axios.post(
+        '/api/admin/data-processing/submit_obj', 
+        {objectType: type, object: object}
+      );
+      console.log(res.data);
+      switch(type){
+        case 'datasetNote':
+          setDatasetNote({...datasetNote, id: String(res.data._id)});
+          break;
+        case 'dataset':
+          setDataset({...dataset, id: String(res.data._id)});
+          break;
+        case 'dataObj':
+          setDataObj({...dataObj, id: String(res.data._id)});
+          break;
+        default:
+          break;
+      }
+    }catch(error){
+      console.log(error)
+    }
+  }
 
   return(
     <StyledAddNewObject>
       <h3>Add new data object to the compendium</h3>
-      <div>
+      <div className='dropdown'>
         <CustomSelect 
           selectOne
           selected={selected}
@@ -43,20 +101,34 @@ const AddNewObject = () => {
           label='Dataset name:'
           value={datasetName} 
           onChange={(e) => {setDatasetName( e.target.value)}}
+          rows={10}
+          cols={100}
         />
       </div>
-      <h4>Add a DatasetNote document</h4>
-      <div>
-        <InputTextarea value={datasetNote} onChange={(e) => setDatasetNote(e.target.value)} rows={10} cols={100} />
-      </div>
-      <h4>Add a Dataset document</h4>
-      <div>
-        <InputTextarea value={dataset} onChange={(e) => setDataset(e.target.value)} rows={30} cols={100} />
-      </div>
-      <h4>Add a DataObject document</h4>
-      <div>
-        <InputTextarea value={dataObj} onChange={(e) => setDataObj(e.target.value)} rows={30} cols={100} />
-      </div>
+      <ObjectTextArea 
+        title='Add a DatasetNote document'
+        submit={submitObject('datasetNote', datasetNote)}
+        object={datasetNote}
+        setObject={setDatasetNote}
+        rows={10} 
+        cols={100} 
+      />
+      <ObjectTextArea 
+        title='Add a Dataset document'
+        submit={submitObject('dataset', dataset)}
+        object={dataset}
+        setObject={setDataset}
+        rows={30} 
+        cols={100} 
+      />
+      <ObjectTextArea 
+        title='Add a DataObject document'
+        submit={submitObject('dataObj', dataObj)}
+        object={dataObj}
+        setObject={setDataObj}
+        rows={30} 
+        cols={100} 
+      />
     </StyledAddNewObject>
   )
 }

client/src/components/Admin/JSONStructures/dataobject.js

@@ -1,9 +1,7 @@
 export const baseDataObject = {
   info: {
     date: {
-      created: {
-        $date: "2023-00-00T00:00:00.000Z"
-      }
+      created: ""
     },
     status: "complete",
     private: false,
@@ -37,9 +35,7 @@ export const baseDataObject = {
   dataObjType: "BaseDataObject",
   datasetType: "",
   name: "",
-  dataset: {
-    $oid: ""
-  },
+  dataset: "",
   repositories: [
     {
       version: "1.0",
@@ -58,9 +54,7 @@ export const baseDataObject = {
 export const genomeDataObject = {
   info: {
     date: {
-      created: {
-        $date: "2023-00-00T00:00:00.000Z"
-      }
+      created: ""
     },
     status: "complete",
     private: false,
@@ -95,9 +89,7 @@ export const genomeDataObject = {
   dataObjType: "GenomeDataObject",
   datasetType: "",
   name: "",
-  dataset: {
-    $oid: ""
-  },
+  dataset: "",
   repositories: [
     {
       version: "3.13",

client/src/components/Admin/JSONStructures/dataset.js

@@ -68,9 +68,7 @@ export const psetDataset = {
       options: []
     }
   ],
-  datasetNote: {
-    $oid: ""
-  },
+  datasetNote: "",
   releaseNotes: {
     counts: [
       {
@@ -103,7 +101,6 @@ export const psetDataset = {
   },
   info: {
     includedData: "sensitivity",
-    pachydermPipeline: "getGDSCv1"
   }
 }
 
@@ -133,9 +130,7 @@ export const genericDataset = {
       options: []
     }
   ],
-  datasetNote: {
-    $oid: ""
-  },
+  datasetNote: "",
   releaseNotes: {
     counts: [
       {
@@ -188,9 +183,7 @@ export const clinicalDataset = {
       options: []
     }
   ],
-  datasetNote: {
-    $oid: ""
-  },
+  datasetNote: "",
   status: {
     unavailable: false,
     disabled: false,

client/src/components/Admin/JSONStructures/datasetnote.js

@@ -1,6 +1,6 @@
 const datasetNote = {
   name: "",
-  disclaimer: "The DatasetName data were re-processed and shared by the Haibe-Kains Lab (University Health Network). The Haibe-Kains Lab has re-annotated the data to maximize overlap with other clinical datasets.",
+  disclaimer: "The data in this dataset were re-processed and shared by the Haibe-Kains Lab (University Health Network). The Haibe-Kains Lab has re-annotated the data to maximize overlap with other clinical datasets.",
   usagePolicy: "The data is under <a href='https://creativecommons.org/licenses/by/4.0/'>Creative Commons Attribution 4.0 International License</a> provided.<br />Source: <a href='https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse15471'>https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse15471</a>",
   citations: [
     ""

client/src/components/Admin/SubComponents/ObjectTextArea.js

@@ -0,0 +1,47 @@
+import React from "react";
+import { InputTextarea } from 'primereact/inputtextarea';
+import { Button } from 'primereact/button';
+import styled from 'styled-components';
+
+const StyledTextArea = styled.div`
+  .submit-button {
+    display: flex;
+    align-items: center;
+    button {
+      margin-right: 10px;
+    }
+    .object-id {
+      font-size: 14px;
+    }
+  }
+`;
+
+const ObjectTextArea = (props) => {
+  const { title, submit, object, setObject, rows, cols, } = props;
+  return(
+    <StyledTextArea>
+      <h4>{title}</h4>
+      <div>
+        <InputTextarea 
+          value={object.text} 
+          onChange={(e) => setObject({...object, text: e.target.value})} 
+          rows={rows} 
+          cols={cols} 
+          style={{whiteSpace: 'pre', overflowWrap: 'normal', overflowX: 'scroll', fontFamily: 'monospace'}}
+        />
+        <div className='submit-button'>
+          <Button 
+            label='Submit' 
+            onClick={submit} 
+          />
+          {
+            object.id.length > 0 &&
+            <div className='object-id'>ID: {object.id}</div>
+          }
+        </div>
+      </div>
+   </StyledTextArea>
+  )
+}
+
+export default ObjectTextArea;

routes/api/view/admin.js

@@ -1,5 +1,7 @@
 const axios = require('axios');
 const DataObject = require('../../../db/models/data-object').DataObject;
+const DatasetNote = require('../../../db/models/dataset-note');
+const Dataset = require('../../../db/models/dataset');
 const dataObjectHelper = require('../../../helper/data-object');
 const timers = require('timers/promises');
 
@@ -146,29 +148,36 @@ const uploadDataObject = async (req, res) => {
     }
 }
 
-const updateSubmission = async (req, res) => {
-    // console.log(req.params.id);
-    // try{
-    //     await dataSubmission.updateOne({_id: mongo.ObjectID(req.params.id)}, {'info.status': 'complete'});
-    // }catch(error){
-    //     console.log(error);
-    //     res.status(500);
-    // }finally{
-    //     res.send();
-    // }
+const submitObject = async (req, res) => {
+    let result = null;
+    try{
+        let objectType = req.body.objectType;
+        let object = JSON.parse(req.body.object.text);
+        switch(objectType){
+            case 'datasetNote':
+                let note = new DatasetNote(object);
+                result = await note.save();
+                break;
+            case 'dataset':
+                let dataset = new Dataset(object);
+                result = await dataset.save();
+                break;
+            case 'dataObj':
+                let dataObj = new DataObject(object);
+                result = await dataObj.save();
+                break;
+            default:
+                break;
+        }
+    }catch(error){
+        console.log(error);
+        res.status(500);
+    }finally{
+        res.send(result)
+    }
 }
 
-const getSubmissionList = async (req, res) => {
-    // let data = []
-    // try{
-    //     data = await dataSubmission.list({}, {'projection': {'info': true}});
-    // }catch(error){
-    //     console.log(error);
-    //     res.status(500);
-    // }finally{
-    //     res.send(data);
-    // }
-}
+
 
 module.exports = {
     canonicalPSets,
@@ -177,6 +186,5 @@ module.exports = {
     runPipeline,
     processedDataObjects,
     uploadDataObject,
-    updateSubmission,
-    getSubmissionList
+    submitObject
 }

routes/router.js

@@ -35,6 +35,7 @@ router.get('/view/admin/pipelines', auth.verifyToken, auth.isAdmin, admin.getPip
 router.post('/admin/data-processing/create-pipeline', auth.verifyToken, auth.isAdmin, admin.createPipeline);
 router.post('/admin/data-processing/run-pipeline', auth.verifyToken, auth.isAdmin, admin.runPipeline);
 router.post('/admin/data-processing/upload_data_obj', auth.verifyToken, auth.isAdmin, admin.uploadDataObject);
+router.post('/admin/data-processing/submit_obj', auth.verifyToken, auth.isAdmin, admin.submitObject);
 
 // data object
 router.get('/data-objects/search', dataObject.search);