Dataset types url

src/src/components/collections/collections.jsx

@@ -97,7 +97,12 @@ export function CollectionForm (props){
           entity.id = entity.uuid;
           //When coming from the Entity, the Datasets use dataset_type, from the Search UI they pass display_subtype instead
           if (entity.dataset_type && entity.dataset_type.length > 0) {
-            var subtype = generateDisplaySubtypeSimple_UBKG(entity.dataset_type[0],props.dtl_all);
+            var subtype = "";
+            if (typeof entity.dataset_type === 'string'){
+              subtype = generateDisplaySubtypeSimple_UBKG(entity.dataset_type,props.dtl_all);
+            }else{
+              subtype = generateDisplaySubtypeSimple_UBKG(entity.dataset_type[0],props.dtl_all);
+            }
             entity.display_subtype = subtype;
           }else {
 

src/src/components/collections/epicollections.jsx

@@ -97,7 +97,12 @@ export function EPICollectionForm (props){
           entity.id = entity.uuid;
           //When coming from the Entity, the Datasets use dataset_type, from the Search UI they pass display_subtype instead
           if (entity.dataset_type && entity.dataset_type.length > 0) {
-            var subtype = generateDisplaySubtypeSimple_UBKG(entity.dataset_type[0],props.dtl_all);
+            var subtype = "";
+            if (typeof entity.dataset_type === 'string'){
+              subtype = generateDisplaySubtypeSimple_UBKG(entity.dataset_type,props.dtl_all);
+            }else{
+              subtype = generateDisplaySubtypeSimple_UBKG(entity.dataset_type[0],props.dtl_all);
+            }
             entity.display_subtype = subtype;
           }else {
 

src/src/components/datasets.jsx

@@ -1,7 +1,7 @@
 import React, { useEffect, useState, useRef, useContext  } from "react";
 import { useParams }from 'react-router-dom';
 import { entity_api_get_entity} from '../service/entity_api';
-import { ubkg_api_get_assay_type_set } from "../service/ubkg_api";
+// import { ubkg_api_get_assay_type_set } from "../service/ubkg_api";
 import DatasetFormLegacy from "./ingest/dataset_edit";
 import {useNavigate} from "react-router-dom";
 import {useLocation } from 'react-router'

src/src/components/ingest/dataset_edit.jsx

@@ -1712,8 +1712,8 @@ name, display_doi, doi
         <option value=""></option>
         {this.props.dtl_all.map((type, index) => {
           return (
-            <option key={index + 1} value={type.term}>
-              {type.term}
+            <option key={index + 1} value={type.dataset_type}>
+              {type.dataset_type}
             </option>
           );
         })}

src/src/components/ingest/publications_edit.jsx

@@ -52,7 +52,7 @@ import {
   entity_api_get_entity,
 } from "../../service/entity_api";
 //import { withRouter } from 'react-router-dom';
-import {ubkg_api_get_assay_type_set} from "../../service/ubkg_api";
+// import {ubkg_api_get_assay_type_set} from "../../service/ubkg_api";
 import {getPublishStatusColor} from "../../utils/badgeClasses";
 import {generateDisplaySubtype} from "../../utils/display_subtypes";
 import {removeEmptyValues} from "../../utils/constants_helper";
@@ -81,7 +81,7 @@ class PublicationEdit extends Component {
     newForm: this.props.newForm,
     dataset_type:"publication",
     dtl_primary: [],
-    dtl_all: [],
+    // dtl_all: [],
     selected_dt: "",
     dataset_info: "",
     description: "",
@@ -215,7 +215,7 @@ class PublicationEdit extends Component {
     //consoledebug("this.state.validationStatus.publication_doi.length >0", this.state.validationStatus.publication_doi.length >0);
     // Modal state as flag for add/remove?
     document.addEventListener("click", this.handleClickOutside);
-    this.setAssayLists();
+    // this.setAssayLists();
     var savedGeneticsStatus = undefined;
     try {
       var auth = JSON.parse(localStorage.getItem("info")).groups_token;
@@ -477,26 +477,26 @@ class PublicationEdit extends Component {
     }
   }
 
-  setAssayLists() {
-    ubkg_api_get_assay_type_set()
-      .then((res) => {
-        this.setState({
-          dtl_all: res.data.result.map((value, index) => {
-            return value.name;
-          }),
-        });
-      })
-      .catch((err) => {});
-    ubkg_api_get_assay_type_set("primary")
-      .then((res) => {
-        this.setState({
-          dtl_primary: res.data.result.map((value, index) => {
-            return value.name;
-          }),
-        });
-      })
-      .catch((err) => {});
-  }
+  // setAssayLists() {
+  //   ubkg_api_get_assay_type_set()
+  //     .then((res) => {
+  //       this.setState({
+  //         dtl_all: res.data.result.map((value, index) => {
+  //           return value.name;
+  //         }),
+  //       });
+  //     })
+  //     .catch((err) => {});
+  //   ubkg_api_get_assay_type_set("primary")
+  //     .then((res) => {
+  //       this.setState({
+  //         dtl_primary: res.data.result.map((value, index) => {
+  //           return value.name;
+  //         }),
+  //       });
+  //     })
+  //     .catch((err) => {});
+  // }
 
   componentWillUnmount() {
     document.removeEventListener("click", this.handleClickOutside, true);
@@ -1888,28 +1888,28 @@ class PublicationEdit extends Component {
   //   }
   // }
 
-  renderAssayColumn(min, max) {
-    // Hijacking Select options based on Primary DT 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);
-      });
-    } else {
-      // false = Not primary DT, set options to full
-      return this.props.dtl_all.slice(min, max).map((val, idx) => {
-        return this.renderAssay(val, idx);
-      });
-    }
-  }
+  // renderAssayColumn(min, max) {
+  //   // Hijacking Select options based on Primary DT 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);
+  //     });
+  //   } else {
+  //     // false = Not primary DT, set options to full
+  //     return this.props.dtl_all.slice(min, max).map((val, idx) => {
+  //       return this.renderAssay(val, idx);
+  //     });
+  //   }
+  // }
 
-  renderAssay(val) {
-    return (
-      <option key={val.name} value={val.name} id={val.name}>
-        {val.description}
-      </option>
-    );
-  }
+  // renderAssay(val) {
+  //   return (
+  //     <option key={val.name} value={val.name} id={val.name}>
+  //       {val.description}
+  //     </option>
+  //   );
+  // }
 
   renderListAssay(val) {
     return <li key={val}>{val}</li>;
@@ -2319,6 +2319,7 @@ class PublicationEdit extends Component {
           <div className="form-group">
           <FormControl fullWidth>
               <TextField
+                required
                 error={this.state.validationStatus.description.length >0}
                 label="Abstract"
                 disabled={!this.state.writeable}

src/src/components/publications.jsx

@@ -1,7 +1,7 @@
 import React, { useEffect, useState, useRef  } from "react";
 import { useParams }from 'react-router-dom';
 import { entity_api_get_entity} from '../service/entity_api';
-import { ubkg_api_get_assay_type_set } from "../service/ubkg_api";
+import { ubkg_api_get_dataset_type_set } from "../service/ubkg_api";
 import PublicationFormLegacy from "./ingest/publications_edit";
 import {useNavigate} from "react-router-dom";
 import { useLocation } from 'react-router'
@@ -77,13 +77,16 @@ export const RenderPublication = (props) => {
 
     function checkAssayType(dtype){
       // These'll likely be changing and it's causing off behavior for publications
-      //  Nuking for now
-      ubkg_api_get_assay_type_set("primary")// the list call only gets primaries for now.
+      //  // Nuking for now
+      // Just swap for the new dataset types call
+
+      // ubkg_api_get_assay_type_set("primary")// the list call only gets primaries for now.
+      ubkg_api_get_dataset_type_set()
       .then((response) => {
         console.debug("checkAssayType Primary", response);
-        setDataTypeList(response.data.result);
-        setDtl_primary(response.data.result);
-        setDtl_all(response.data.result);
+        setDataTypeList(response);
+        setDtl_primary(response);
+        setDtl_all(response);
         setDtl_status(true);
         setIsLoadingDTList(0);
       }) 

src/src/service/search_api.js

@@ -263,29 +263,6 @@ export function search_api_get_assay_type(assay) {
     });
 }
 
-export function search_api_get_assay_list(params) {
-  // So the api defaults to primary even if False is passed as ?primary=false
-  var primaryParam = {};
-  if (params) {
-    primaryParam = { params: params };
-  }
-  return (
-    axios
-      // Only regards flag via url for some reason?
-      .get(`${process.env.REACT_APP_SEARCH_API_URL}/assaytype?primary=true`)
-      .then((res) => {
-        let data = res.data;
-        let dtListMapped = data.result.map((value, index) => {
-          return value;
-        });
-        return { status: res.status, data: dtListMapped };
-      })
-      .catch((error) => {
-        return { error };
-      })
-  );
-}
-
 export function search_api_get_assay_set(scope) {
   // Scope informs either Primary, Alt, or All
   var target = "";

src/src/service/ubkg_api.js

@@ -19,31 +19,31 @@ import { stripHTML,toTitleCase } from '../utils/string_helper'
  *
  * return:  { status, results}
  */
-export function ubkg_api_get_assay_type_set(scope) {
-  // application_context 
-  // console.debug("ubkg_api_get_assay_type_set", scope);
-  let url = `${process.env.REACT_APP_UBKG_API_URL}/assaytype?application_context=HUBMAP`;
-  // let url = `${process.env.REACT_APP_SEARCH_API_URL}/v3/assaytype`;
-  // Note: scope == 'all' will not include the query parameter
-  if (scope === 'primary') {
-      url += '&primary=true'
-  } else if (scope === 'alt') {
-      url += '&primary=false'
-  }
-  // console.debug("ubkg_api_get_assay_type_set url", url);
-  return axios
-    .get(url)
-      .then(res => {
-        // let mapCheck = data.result.map((value, index) => { return value });
-        let data = res.data;
-        return {data}
-      })
-      .catch(error => {
-        console.debug('%c⭗', 'color:#ff005d', "ubkg_api_get_assaytype", error, error.response);
-        var errorResp = captureError(error);
-        return errorResp
-      });
-};
+// export function ubkg_api_get_assay_type_set(scope) {
+//   // application_context 
+//   // console.debug("ubkg_api_get_assay_type_set", scope);
+//   let url = `${process.env.REACT_APP_UBKG_API_URL}/assaytype?application_context=HUBMAP`;
+//   // let url = `${process.env.REACT_APP_SEARCH_API_URL}/v3/assaytype`;
+//   // Note: scope == 'all' will not include the query parameter
+//   if (scope === 'primary') {
+//       url += '&primary=true'
+//   } else if (scope === 'alt') {
+//       url += '&primary=false'
+//   }
+//   // console.debug("ubkg_api_get_assay_type_set url", url);
+//   return axios
+//     .get(url)
+//       .then(res => {
+//         // let mapCheck = data.result.map((value, index) => { return value });
+//         let data = res.data;
+//         return {data}
+//       })
+//       .catch(error => {
+//         console.debug('%c⭗', 'color:#ff005d', "ubkg_api_get_assaytype", error, error.response);
+//         var errorResp = captureError(error);
+//         return errorResp
+//       });
+// };
 
 /*
  * UBKG GET organtype/all method
@@ -71,7 +71,8 @@ export function ubkg_api_get_organ_type_set() {
  *
  */
 export function ubkg_api_get_dataset_type_set() {
-  let url = `${process.env.REACT_APP_UBKG_API_URL}/valueset?parent_sab=HUBMAP&parent_code=C003041&child_sabs=HUBMAP`;
+  // let url = `${process.env.REACT_APP_UBKG_API_URL}/valueset?parent_sab=HUBMAP&parent_code=C003041&child_sabs=HUBMAP`;
+  let url = `${process.env.REACT_APP_UBKG_API_URL}/dataset-types?application_context=HUBMAP`;
   return axios
     .get(url)
       .then(res => {

src/src/utils/display_subtypes.jsx

@@ -7,7 +7,7 @@
 // otherwise the display name linked to the value of the corresponding description of specimen_type code
 // Dataset: the display names linked to the values in dataset_type as a comma separated list
 
-import { ubkg_api_get_organ_type_set,ubkg_api_get_assay_type_set } from "../service/ubkg_api";
+import { ubkg_api_get_organ_type_set,ubkg_api_get_dataset_type_set } from "../service/ubkg_api";
 import { SAMPLE_TYPES } from "../constants";
 
 
@@ -134,23 +134,23 @@ function get_organ_description_UBKG(organ_code) {
 }
 
 // Get Sample Types
-function get_sample_types_UBKG(tissue_code){
-  ubkg_api_get_assay_type_set()
-    .then((res) => {
-      console.debug('%c⊙', 'color:#00ff7b', res);
-      return res;
-    })
-    .catch((error) => {
-      console.error('%c⭗', 'color:#ff005d', "ERROR: ubkg_api_get_organ_type_set",error);
-    });
+// function get_sample_types_UBKG(tissue_code){
+//   ubkg_api_get_assay_type_set()
+//     .then((res) => {
+//       console.debug('%c⊙', 'color:#00ff7b', res);
+//       return res;
+//     })
+//     .catch((error) => {
+//       console.error('%c⭗', 'color:#ff005d', "ERROR: ubkg_api_get_organ_type_set",error);
+//     });
 
- }
-function get_sample_description_UBKG(tissue_code) {
-  var typeList = get_sample_types_UBKG();
-  console.debug('%c⊙', 'color:#00ff7b', "typeList",typeList );
-   console.debug("get_organ_description",typeList[tissue_code]);
-   return "TEST";
- }
+//  }
+// function get_sample_description_UBKG(tissue_code) {
+//   var typeList = get_sample_types_UBKG();
+//   console.debug('%c⊙', 'color:#00ff7b', "typeList",typeList );
+//    console.debug("get_organ_description",typeList[tissue_code]);
+//    return "TEST";
+//  }
 
 
 export function generateDisplaySubtype( entity) {
@@ -194,10 +194,9 @@ export function generateDisplaySubtype( entity) {
 
 
 export function generateDisplaySubtypeSimple_UBKG(datatype, datatypeList) {
-  // console.debug('%c⊙', 'color:#00ff7b', "generateDisplaySubtypeSimple_UBKG", datatype, datatypeList);
-  const assayDetail = datatypeList.find(({ term }) => term === datatype);
-  if (assayDetail !==undefined && assayDetail && assayDetail.term) {
-    return assayDetail.term
+  const assayDetail = datatypeList.find(({ dataset_type }) => dataset_type === datatype);
+  if (assayDetail !==undefined && assayDetail && assayDetail.dataset_type) {
+    return assayDetail.dataset_type
   } else {
     return "N/A"
   }