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Merge pull request #1413 from hubmapconsortium/ruiData
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Fix population of data being sent to RUI for Input initilizations
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@yuanzhou
yuanzhou authored May 29, 2024
2 parents fc01373 + a7872ef commit d52383e
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Showing 3 changed files with 102 additions and 35 deletions.
3 changes: 2 additions & 1 deletion src/src/components/uuid/tissue_form_components/ruiIntegration.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,8 @@ class RUIIntegration extends Component {
}

updateRUIConfig() {
console.debug('%c◉ thisPROPS RuiInt ', 'color:#00ff7b',this.props.organ, this.props.organList,this.props.organList[this.props.organ] );
// console.debug('%c◉ thisPROPS RuiInt ', 'color:#00ff7b',this.props.organ, this.props.organList,this.props.organList[this.props.organ] );
console.debug('%c◉ thisPROPS RuiInt ', 'color:#00ff7b', this.props );
const organ_id = RUI_ORGAN_MAPPING[this.props.organ];
const organ_info = this.props.organList[this.props.organ].split("(");
const organ_name = organ_info[0].toLowerCase().trim();
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108 changes: 74 additions & 34 deletions src/src/components/uuid/tissue_form_components/tissueForm.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,8 @@ import { entity_api_get_entity,
entity_api_update_entity,
entity_api_create_entity,
entity_api_create_multiple_entities,
entity_api_get_entity_ancestor
entity_api_get_entity_ancestor,
entity_api_get_entity_ancestor_list
} from '../../../service/entity_api';
import { ingest_api_allowable_edit_states, ingest_api_all_user_groups, ingest_api_get_associated_ids } from '../../../service/ingest_api';
// import { useHistory } from "react-router-dom";
Expand Down Expand Up @@ -346,7 +347,7 @@ class TissueForm extends Component {
file_uuid: thumbnail_file.file_uuid
});
} catch {}

this.setState(
{
author: this.state.editingEntity.created_by_user_email,
Expand Down Expand Up @@ -374,14 +375,15 @@ class TissueForm extends Component {
rui_show_btn: true
}, () => {
console.debug('%c◉ RUISHOW ', 'color:#00ff7b');
})
})
}
})

if(this.state.editingEntity.direct_ancestor.entity_type === "Donor" || this.state.editingEntity.direct_ancestor.entity_type === "Organ"){
this.getSourceAncestorOrgan(this.state.editingEntity);
}

this.fetchDonorMeta(this.props.editingEntity.uuid);


} else {
Expand All @@ -404,6 +406,44 @@ class TissueForm extends Component {

}



fetchDonorMeta(sourceUUID){
// Lets get the donor metadata to sort our values for the RUI
entity_api_get_entity_ancestor_list(sourceUUID, JSON.parse(localStorage.getItem("info")).groups_token)
.then((res) => {
console.debug('%c◉ ANCESTOR LIST ', 'color:#8C00FF', res.results);
var donor;
if (res.results.length === 1) { //Must be an organ source, so this ancestor must be the donor
donor = res.results[0]
}else{
donor = res.results.filter(d => d.entity_type === "Donor");
donor = donor[0]
}

console.debug('%c◉ donor ', 'color:#00ff7b', donor);
var donorMeta = donor.metadata.organ_donor_data ? donor.metadata.organ_donor_data : donor.metadata.living_donor_data;
console.debug('%c◉ donorMeta ', 'color:#4400FF', donorMeta);
var donorSexDetails = donorMeta.filter(m => m.grouping_code === "57312000");
// var donorSexDetails = donorMeta.filter(m => m.data_value === "Sex");
console.debug('%c◉ donorSexDetails ', 'color:#0011FF', donorSexDetails);
var donorSex = donorSexDetails[0].preferred_term;
console.debug('%c◉ donorSex ', 'color:#0077FF', donorSex);
// return (donorSex ? donorSex : undefined);
this.setState({
donor_sex: donorSex,
sex: donorSex
}, () => {
// console.debug('%c◉ Donor Meta Loaded ', 'color:#00ff7b', );
})
})
.catch((err) =>{
console.debug("ERR entity_api_get_entity_ancestor_list",err);
// throw new Error("ERR entity_api_get_entity_ancestor_list");
})
}


fetchOrganTypes(){
ubkg_api_get_organ_type_set()
.then((res) => {
Expand Down Expand Up @@ -627,7 +667,7 @@ class TissueForm extends Component {
}
}));
} else if (!validateProtocolIODOI(value)) {

console.debug('%c◉ validateProtocolIODOI ', 'color:#ff005d',value );
this.setState(prevState => ({
formErrors: {
...prevState.formErrors,
Expand All @@ -646,7 +686,7 @@ class TissueForm extends Component {
this.setState(prevState => ({
formErrors: {
...prevState.formErrors,
protocol_url: "required"
protocol_url: ""
}
}));
}
Expand Down Expand Up @@ -1432,8 +1472,6 @@ handleAddImage = () => {

handleLookUpClick = () => {
//


if (!this.state.lookUpCancelled) {
this.setState({
LookUpShow: true
Expand All @@ -1446,7 +1484,7 @@ handleAddImage = () => {
this.setState({
lookUpCancelled: false
});
}
}

hideLookUpModal = () => {

Expand All @@ -1472,42 +1510,41 @@ handleAddImage = () => {
// Callback for the SOURCE for table selection
handleSelectClick = selection => {
let ancestor_organ = ""



if (selection) {
// check to see if we have an "top-level" ancestor

// Organ added to the Column results for Samples, can pluck it from row.organ now!
// For Ancestry-reasons, we should still check for the top-level ancestor
entity_api_get_entity_ancestor( selection.row.uuid, JSON.parse(localStorage.getItem("info")).groups_token)
.then((response) => {
// console.debug("selection", selection);
// console.debug("handleSelectClick: selection.row.uuid: " + selection.row.uuid, selection.row.organ);
// console.debug("handleSelectClick: response.status: " + response.status);

if (response.status === 200) {
if (response.results.length > 0) {
ancestor_organ = response.results[0].organ; // use "top" ancestor organ
}
} else if (response.error === "400 Bad Request: Unable to get the ancestor organ of an organ.") {
ancestor_organ = selection.row.organ; // the error otherwise crashes
} else {
ancestor_organ = selection.row.organ; // use the direct ancestor
ancestor_organ = selection.row.organ; // use the direct ancestor
}

this.setState({
source_uuid: selection.row.hubmap_id,
source_entity: selection.row,
source_uuid_list: selection.row.uuid, // just add the single for now
source_entity_type: selection.row.entity_type,
organ: ancestor_organ,
ancestor_organ: ancestor_organ, // save the acestor organ for the RUI check
sex: this.getGender(selection.row)
}, () => {
});
this.cancelLookUpModal();

// SETS SEX VALUES BEING PASSED TO RUI
this.fetchDonorMeta(selection.row.uuid);

this.setState({
source_uuid: selection.row.hubmap_id,
source_entity: selection.row,
source_uuid_list: selection.row.uuid, // just add the single for now
source_entity_type: selection.row.entity_type,
organ: ancestor_organ,
ancestor_organ: ancestor_organ, // save the acestor organ for the RUI check
// sex: this.getGender(selection.row)
// sex: this.fetchDonorMeta(selection.row.uuid)
}, () => {
console.debug('%c◉ SETDONORSEX ', 'color:#7BFF00', this.state.sex);
});

this.cancelLookUpModal();
});
}
};

Expand Down Expand Up @@ -2216,7 +2253,8 @@ handleAddImage = () => {
// organList={this.fetchOrganTypes}
organ={ this.state.ancestor_organ ? this.state.ancestor_organ : this.state.source_entity.organ}
// organ={ this.props.editingEntity.organ ? this.props.editingEntity.organ}
sex={this.state.source_entity.sex}
// sex={this.state.source_entity.sex}
sex={this.state.donor_sex}
user={this.state.source_entity.created_by_user_displayname}
location={this.state.rui_location}
parent="TissueForm" />
Expand Down Expand Up @@ -2307,7 +2345,8 @@ handleAddImage = () => {
<RUIIntegration handleJsonRUI={this.handleRUIJson}
organList={this.state.organ_types}
organ={this.props.editingEntity.organ}
sex={this.state.source_entity.sex}
// sex={this.state.source_entity.sex}
sex={this.state.donor_sex}
user={this.state.source_entity.created_by_user_displayname}
location={this.state.rui_location}
parent="TissueForm" />
Expand Down Expand Up @@ -2361,7 +2400,8 @@ handleAddImage = () => {
<RUIIntegration handleJsonRUI={this.handleRUIJson}
organList={this.state.organ_types}
organ={this.props.editingEntity.organ}
sex={this.state.source_entity.sex}
// sex={this.state.source_entity.sex}
sex={this.state.donor_sex}
user={this.state.source_entity.created_by_user_displayname}
location={this.state.rui_location}
parent="TissueForm" />
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26 changes: 26 additions & 0 deletions src/src/service/entity_api.js
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Original file line number Diff line number Diff line change
Expand Up @@ -177,6 +177,32 @@ export function entity_api_get_entity_ancestor(uuid, auth) {
});
};

/*
* get ancestor list for the specified Entity
*
* return: { status, results}
*/
export function entity_api_get_entity_ancestor_list(uuid, auth) {
const options = {
headers: {
Authorization:
"Bearer " + auth,
"Content-Type": "application/json"
}
};
let url = `${process.env.REACT_APP_ENTITY_API_URL}/ancestors/${uuid}`;
return axios
.get(url,options)
.then(res => {
// console.debug(res);
let results = res.data;
return {status: res.status, results: results}
})
.catch(error => {
return {error}
});
};

/*
* get Globus URL
*
Expand Down

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