Merge pull request #1011 from hubmapconsortium/sample-categories

Fix New Dataset Registration & DataProvider on Submit/Modal
hubmapconsortium · Dec 21, 2022 · f59ea2e · f59ea2e
2 parents d860878 + 186dfbd
commit f59ea2e
Show file tree

Hide file tree

Showing 6 changed files with 96 additions and 194 deletions.
diff --git a/src/src/App.js b/src/src/App.js
@@ -23,7 +23,7 @@ import DialogTitle from '@mui/material/DialogTitle';
 
 import AnnouncementTwoToneIcon from '@mui/icons-material/AnnouncementTwoTone';
 import { ingest_api_users_groups } from './service/ingest_api';
-import {search_api_get_assay_list} from "./service/search_api";
+import {search_api_get_assay_list, search_api_get_assay_set} from "./service/search_api";
 import {DataProviders} from "./utils/userInfo";
 
 // import {ErrBox} from "../utils/ui_elements";
@@ -55,6 +55,8 @@ export function App (props){
  var [timerStatus, setTimerStatus] = useState(true);
  var [isLoading, setIsLoading] = useState(true);
  var [dataTypeList, setDataTypeList] = useState({});
+ var [dataTypeListAll, setDataTypeListAll] = useState({});
+ var [dataTypeListPrimary, setDataTypeListPrimary] = useState({});
  var [userGroups, setUserGroups] = useState({});
  var [userDataGroups, setUserDataGroups] = useState({});
  let navigate = useNavigate();
@@ -95,23 +97,32 @@ export function App (props){
  setGroupsToken(JSON.parse(localStorage.getItem("info")).groups_token);
  setAuthStatus(true);
  setTimerStatus(false);
- // console.debug("groupsToken",groupsToken);
 
- // The Dataset Form for New entites loads through the Form
- search_api_get_assay_list()
+ // console.debug("groupsToken",groupsToken);
+ search_api_get_assay_set("primary") // @TODO: Apply to dataset wrapper too? 
  .then((response) => {
- // console.debug("fetchPrimaryDataTypes Response", response);
- let data = response.data;
- setDataTypeList(data);
- setIsLoading(false)
- // console.debug("isLoading", isLoading); 
+ let dtypes = response.data.result;
+ setDataTypeList(dtypes);
+ setDataTypeListPrimary(dtypes);
+ // setIsLoading(false)
+ search_api_get_assay_set()
+ .then((response) => {
+ let dataAll = response.data.result;
+ setDataTypeListAll(dataAll);
+ setIsLoading(false)
+ })
+ .catch(error => {
+ console.debug("fetch DT list Response Error", error);
+ setIsLoading(false)
+ });
  })
  .catch(error => {
- // console.debug("fetch DT list Response Error", error);
+ console.debug("fetch DT list Response Error", error);
  setIsLoading(false)
- // return error;
- // passError(error.status, error.response );
  });
+
+ // The Dataset Form for New entites loads through the Form
+
  // return dt_dict;
 
 
@@ -291,7 +302,7 @@ export function App (props){
  <Route path="/new">
  <Route index element={<SearchComponent />} />
  <Route path='donor' element={ <Forms formType='donor' onReturn={onClose} handleCancel={handleCancel} />}/>
- <Route path='dataset' element={<Forms formType='dataset' dataTypeList={dataTypeList} new='true' onReturn={onClose} handleCancel={handleCancel} /> }/> 
+ <Route path='dataset' element={<Forms formType='dataset' dataTypeList={dataTypeList} dtl_all={dataTypeListAll} dtl_primary={dataTypeListPrimary}new='true' onReturn={onClose} handleCancel={handleCancel} /> }/> 
  <Route path='sample' element={<Forms formType='sample' onReturn={onClose} handleCancel={handleCancel} /> }/> 
 
 {/* 

diff --git a/src/src/assets/Documents/example-sample-registrations.tsv b/src/src/assets/Documents/example-sample-registrations.tsv
@@ -1,2 +1,2 @@
-source_id lab_id sample_type organ_type sample_protocol description rui_location
-HBM749.QJZK.937 19-002 Thymus CC-1 Block D organ_piece https://dx.doi.org/10.17504/protocols.io.8nzhvf6 Test Desc 
+source_id lab_id sample_category organ_type sample_protocol description rui_location
+HBM749.QJZK.937 19-002 Thymus CC-1 Block D block https://dx.doi.org/10.17504/protocols.io.8nzhvf6 Test Desc 
diff --git a/src/src/components/ingest/dataset_edit.jsx b/src/src/components/ingest/dataset_edit.jsx
@@ -133,9 +133,15 @@ class DatasetEdit extends Component {
  document.addEventListener("click", this.handleClickOutside);
  this.setAssayLists();
  var savedGeneticsStatus = undefined;
- const auth = "";
+ try {
+ var auth = JSON.parse(localStorage.getItem("info")).groups_token;
+ } catch {
+ console.debug("LOCALSTROAGE Parse Fai")
+ var auth = "";
+ }
+
  if (localStorage.getItem("info")){
- const auth = JSON.parse(localStorage.getItem("info")).groups_token;
+
  const config = {
  headers: {
  Authorization:
@@ -144,6 +150,7 @@ class DatasetEdit extends Component {
  },
  };
  }else{
+ console.debug("No Auth Token");
  localStorage.setItem("isAuthenticated", false);
  }
 
@@ -176,12 +183,16 @@ class DatasetEdit extends Component {
 
  ingest_api_users_groups(auth)
  .then((res) => {
+ console.debug("groups", res.results);
  const groups = res.results.filter(
  g => g.data_provider === true
  );
+ console.debug("groups", groups);
  this.setState({
  groups: groups,
  groups_dataprovider: groups,
+ },() => {
+ console.debug("groups_dataprovider", this.state.groups_dataprovider);
  });
  })
  .catch((err) => {
@@ -1631,8 +1642,8 @@ class DatasetEdit extends Component {
 
  renderAssayColumn(min, max) {
  // Hijacking Select options based on Primary DT status
- console.debug(this.props.dtl_status);
- if(this.props.dtl_status) { // true = primary dt, set options to primary
+ // console.debug(this.props.dtl_status);
+ if(this.props.dtl_status || this.props.newForm) { // true = primary dt, set options to primary
  return (
  this.props.dtl_primary.slice(min, max).map((val, idx) =>
  {return this.renderAssay(val, idx)})
@@ -1687,6 +1698,9 @@ class DatasetEdit extends Component {
  var len = 0;
  // var dtlistLen = this.props.dataTypeList.length;
  var dtlistLen = this.state.dataTypeDropdown.length;
+ if(this.props.newForm){
+ dtlistLen = this.props.dtl_primary.length;
+ }
  if(this.props.editingDataset && this.props.editingDataset.data_types) {
  //console.debug("this.props.editingDataset", this.props.editingDataset);
  len = this.props.editingDataset.data_types.length;

diff --git a/src/src/components/uuid/forms.jsx b/src/src/components/uuid/forms.jsx
@@ -75,16 +75,35 @@ class Forms extends Component {
  UNSAFE_componentWillMount() {
  console.debug("UNSAFE_componentWillMount");
  // console.debug("dtlist",this.props.dataTypeList);
- var DTList = this.props.dataTypeList;
- console.debug("prepDatatypes", this.prepDatatypes(), DTList);
+ // search_api_get_assay_set()
+ // .then((response) => {
+ // let allDTs = response.data.result;
+ // var DTList = this.props.dataTypeList;
+ // console.debug("prepDatatypes", this.prepDatatypes(), DTList);
+ // this.setState({
+ // dataTypeList: allDTs
+ // }, () => { 
+ // console.debug("FORMS UNSAFE_componentWillMount", this.state);
+ // });
+ // })
+ // .catch(error => {
+ // console.debug("fetch DT list Response Error", error);
+ // // passError(error.status, error.response );
+ // return error;
+
+ // })
+
 
+ var DTList = this.props.dtl_primary;
+ console.debug("unsafeCOMPONENTWILLMOUNT", DTList);
+
  this.setState({
  formType: this.props.formType,
  open: true,
  dataTypeList: DTList
  }, () => { 
-  this.setState({ isLoading: false });
-  console.debug("FORMS componentWillMount", this.state);
+ this.setState({ isLoading: false });
+ console.debug("FORMS componentWillMount", this.state);
  });
  }
 
@@ -230,13 +249,17 @@ class Forms extends Component {
  );
  } else if (this.props.formType === "dataset" ) {
  console.debug("NEW DATASET");
+
  return (
  <DatasetEdit
  dataTypeList={this.props.dataTypeList}
  onCreated={this.onCreated}
  onReturn={this.props.handleCancel}
  changeLink={this.onChangeGlobusLink.bind(this)}
  newForm={true}
+ dtl_primary={this.props.dtl_primary}
+ dtl_all={this.props.dtl_all}
+ dtl_status={false}
  editingDataset="{}"
  />