Merge pull request #711 from hubmapconsortium/test-release

v2.1.3 release
hubmapconsortium · Nov 15, 2021 · 8b67b22 · 8b67b22
2 parents 42a6eb7 + 69ceec4
commit 8b67b22
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Showing 6 changed files with 185 additions and 49 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.1.2
+2.1.3
diff --git a/src/package.json b/src/package.json
@@ -1,6 +1,6 @@
 {
  "name": "ingest-ui",
- "version": "2.1.2",
+ "version": "2.1.3",
  "private": true,
  "homepage": ".",
  "dependencies": {

diff --git a/src/src/components/ingest/dataset_edit.jsx b/src/src/components/ingest/dataset_edit.jsx
@@ -121,7 +121,7 @@ class DatasetEdit extends Component {
  get_assay_type(other_dt, JSON.parse(localStorage.getItem("info")).nexus_token)
  .then((resp) => {
  if (resp.status === 200) {
- console.log('Assay Type info...', resp.results);
+ //console.log('Assay Type info...', resp.results);
 
  if (resp.results) {
  this.setState({
@@ -150,7 +150,7 @@ class DatasetEdit extends Component {
  ingest_api_allowable_edit_states(this.props.editingDataset.uuid, JSON.parse(localStorage.getItem("info")).nexus_token)
  .then((resp) => {
  if (resp.status === 200) {
- console.log('edit states...', resp.results);
+ //console.log('edit states...', resp.results);
 
  this.setState({
  writeable: resp.results.has_write_priv,
@@ -448,7 +448,7 @@ class DatasetEdit extends Component {
  break;
  }
  if (id.startsWith("dt")) {
- //////console.log('ping!', id);
+ console.log('ping!', id);
  if (id === "dt_other") {
  const data_types = this.state.data_types;
  this.setState({
@@ -469,7 +469,38 @@ class DatasetEdit extends Component {
  }
  } else {
  //////console.log(id, e.target.checked)
- if (e.target.checked) {
+ if (value === "other") {
+ const data_types = this.state.data_types;
+ data_types.clear();
+ data_types.add(value);
+ this.setState({
+ data_types: data_types,
+ has_other_datatype: value === "other",
+ });
+ console.log("other", this.state.has_other_datatype);
+ if (value !== "other") {
+ const data_type_options = new Set(this.state.data_type_dicts.map((elt, idx) => {return elt.name}));
+ const data_types = this.state.data_types;
+ const other_dt = Array.from(data_types).filter(
+ (dt) => !data_type_options.has(dt)
+ )[0];
+ data_types.delete(other_dt);
+ this.setState({
+ data_types: data_types,
+ other_dt: "",
+ });
+ }
+
+ } else {
+ const data_types = this.state.data_types;
+ data_types.clear();
+ data_types.add(value);
+ this.setState({
+ has_other_datatype: false,
+ data_types: data_types,
+ });
+ console.log("data types is ", data_types);
+ }/*if (e.target.checked) {
  const data_types = this.state.data_types;
  data_types.add(name);
  this.setState({
@@ -481,7 +512,7 @@ class DatasetEdit extends Component {
  this.setState({
  data_types: data_types,
  });
- }
+ }*/
 
  }
  //////console.log('data_types', this.state.data_types)
@@ -1376,8 +1407,10 @@ class DatasetEdit extends Component {
 
  renderOneAssay(val, idx) {
  var idstr = 'dt_' + val.name.toLowerCase().replace(' ','_');
- return (<div className='form-group form-check ' key={idstr}>
- <input type='checkbox' className={'form-check-input '+ this.errorClass(this.state.formErrors.data_types)} name={val.name} key={idstr} id={idstr}
+
+ return (<div className='form-group form-check' key={idstr}>
+ <input type='radio' className='form-check-input' name={val.name} key={idstr} id={idstr}
+
  onChange={this.handleInputChange} checked={this.state.data_types.has(val.name)}
  />
  <label className='form-check-label' htmlFor={idstr}>{val.description}</label>
@@ -1407,49 +1440,105 @@ class DatasetEdit extends Component {
  }
 
  renderAssayColumn(min, max) {
- return (<div>
- {this.state.data_type_dicts.slice(min, max).map((val, idx) =>
- {return this.renderOneAssay(val, idx)})}</div>
+ return (
+ this.state.data_type_dicts.slice(min, max).map((val, idx) =>
+ {return this.renderAssay(val, idx)})
  )
  }
+
+ renderAssay(val, idx) {
+ var idstr = 'dt_' + val.name.toLowerCase().replace(' ','_');
+ return (
+ <option value={val.name} onChange={this.handleInputChange} id={idstr}>{val.description}</option>
+ )
+ }
+
+ renderListAssay(val) {
+ return (
+ <li>{val}</li>
+ )
+ }
+
+ renderMultipleAssays() {
+ var arr = Array.from(this.state.data_types)
+ return (
+ arr.map((val) =>
+ {return this.renderListAssay(val)})
+ )
+ }
+
+
+
+
 
  renderAssayArray() {
  if (this.state.data_type_dicts.length) {
  var len = this.state.data_type_dicts.length;
- var entries_per_col = Math.ceil(len / 3);
+ //var entries_per_col = Math.ceil(len / 3);
  //var num_cols = Math.ceil(len / entries_per_col);
- return (<>
- <div className='col-sm-4'> {this.renderAssayColumn(0, entries_per_col)} </div>
- <div className='col-sm-4'> {this.renderAssayColumn(entries_per_col, 2*entries_per_col)} </div>
- <div className='col-sm-4'> {this.renderAssayColumn(2*entries_per_col, len+1)}
- <div className='form-group form-check'>
- <input
- type='checkbox'
- className='form-check-input '
- name='dt_other'
- id='dt_other'
- onChange={this.handleInputChange}
- checked={this.state.has_other_datatype}
- />
- <label className='form-check-label' htmlFor='dt_other'>
- Other
- </label>
- </div>
- {this.state.has_other_datatype && (
+ console.log("length is ", this.state.data_types.size)
+ console.log("other ", this.state.has_other_datatype)
+
+ if (this.state.data_types.size === 1 && this.state.has_other_datatype) {
+ console.log("runs")
+ return (<>
+
+ <select value={this.state.data_types.values().next().value} id="dt_select" onChange={this.handleInputChange}>
+ <option></option>
+ {this.renderAssayColumn(0, len)}
+ <option value="other">Other</option>
+ </select>
+
+ {this.state.has_other_datatype && (
+
  <div className='form-group'>
  <input type='text' name='other_dt' id='other_dt'
-  className={"form-control " +
-  this.errorClass(this.state.formErrors.other_dt)
-  }
-  placeholder='Other Data Type'
-  value={this.state.other_dt}
-  onChange={this.handleInputChange}
-  />
+  className={"form-control " +
+  this.errorClass(this.state.formErrors.other_dt)
+  }
+  placeholder='Other Data Type'
+  value={this.state.other_dt}
+  onChange={this.handleInputChange}
+  />
  </div>
- )}
- </div>
- </>
- )
+ )}
+ </>
+ )
+ } else if (this.state.data_types.size === 1 || this.state.data_types.size === 0) {
+
+ return (<>
+
+ <select value={this.state.data_types.values().next().value} id="dt_select" onChange={this.handleInputChange}>
+ <option></option>
+ {this.renderAssayColumn(0, len)}
+ <option value="other">Other</option>
+ </select>
+
+ {this.state.has_other_datatype && (
+
+ <div className='form-group'>
+ <input type='text' name='other_dt' id='other_dt'
+ className={"form-control " +
+ this.errorClass(this.state.formErrors.other_dt)
+ }
+ placeholder='Other Data Type'
+ value={this.state.other_dt}
+ onChange={this.handleInputChange}
+ />
+ </div>
+ )}
+ </>
+ )
+ } else if (this.state.data_types.size > 1) {
+ return (<>
+
+ <ul>
+ {this.renderMultipleAssays()}
+ </ul>
+
+ </>)
+ }
+
  }
  else {
  return <h3>Loading assay types...</h3>;
@@ -1843,7 +1932,7 @@ class DatasetEdit extends Component {
  <div className='col-sm-12'>
  {this.state.formErrors.data_types && (
  <div className='alert alert-danger'>
- At least one Dataa Type is Required.
+ At least one Data Type is Required.
  </div>
  )}
  </div>

diff --git a/src/src/components/search/SearchComponent.jsx b/src/src/components/search/SearchComponent.jsx
@@ -15,7 +15,7 @@ import { COLUMN_DEF_DONOR, COLUMN_DEF_SAMPLE, COLUMN_DEF_DATASET, COLUMN_DEF_UPL
 
 import { entity_api_get_entity } from '../../service/entity_api';
 import { ingest_api_allowable_edit_states, ingest_api_users_groups } from '../../service/ingest_api';
-import 'url-search-params-polyfill';
+// import 'url-search-params-polyfill';
 
 // Creation donor_form_components
 

diff --git a/src/src/components/uploads/editUploads.jsx b/src/src/components/uploads/editUploads.jsx
@@ -24,7 +24,9 @@ import TableHead from '@material-ui/core/TableHead';
 import TableRow from '@material-ui/core/TableRow';
 import { ingest_api_get_globus_url, 
  ingest_api_validate_upload,
- ingest_api_submit_upload } from '../../service/ingest_api';
+ ingest_api_submit_upload,
+ ingest_api_users_groups } from '../../service/ingest_api';
+//import { GROUPS } from '../../service/groups'
 import { COLUMN_DEF_DATASET} from '../search/table_constants';
 
 class EditUploads extends Component {
@@ -370,13 +372,20 @@ class EditUploads extends Component {
 
  renderButtonBar(){
  return (
- <div className='row'>
+ <div className='row justify-content-end'>
  <div className="col-sm-12">
  <Divider />
  </div>
 
  {this.renderHelperText()}
- <div className='col-md-12 text-right pads'>
+
+ <div className='col-md-2 pads'>
+ {this.renderValidateButton()}
+ </div>
+
+
+ <div className='col-md-1 pads'>
+
  {this.renderActionButton()}
  <button
  type='button'
@@ -390,8 +399,46 @@ class EditUploads extends Component {
  );
  } 
 
+ renderValidateButton() {
+ var local = JSON.parse(localStorage.getItem("info"));
+ var group_uuids = ["89a69625-99d7-11ea-9366-0e98982705c1", "75804b96-d4a8-11e9-9da9-0ad4acb67ed4"];
+ console.log(group_uuids.length);
+ ingest_api_users_groups(local.nexus_token).then((results) => {
+ console.log(results.results);
+ });
+ if (["SUBMITTED", "INVALID", "ERROR"].includes(
+ this.state.status.toUpperCase()
+ )){
+ ingest_api_users_groups(local.nexus_token).then((results) => {
+ if (results.status === 200) {
+ results.results.forEach(function(result) {
+ if (group_uuids.includes(result.uuid)) {
+ return (
+ <React.Fragment>
+ <button 
+ type='button'
+ className = 'btn btn-info mr-1'
+ onClick = {() => this.tempAlert()}
+ >
+ Validate
+ </button>
+ </React.Fragment>
+ )
+ }
+ }
+ )
+ }
+ });
+ }
+ }
+
+ tempAlert() {
+ window.alert("This function has not yet been implemented.");
+ }
 
  renderActionButton() {
+ var local = JSON.parse(localStorage.getItem("info"));
+ console.debug(local);
  if (["NEW", "INVALID", "ERROR"].includes(
  this.state.status.toUpperCase()
  )){

diff --git a/src/src/components/uuid/tissue_form_components/tissueForm.jsx b/src/src/components/uuid/tissue_form_components/tissueForm.jsx
@@ -321,7 +321,7 @@ class TissueForm extends Component {
 
  } );
 
- this.getSourceAncestorOrgan(this.state.editingEntity);
+ //this.getSourceAncestorOrgan(this.state.editingEntity);
 
 
  } else {
@@ -505,7 +505,7 @@ class TissueForm extends Component {
  //////console.debug('Entity ancestors...', response.results);
  if (response.results.length > 0) {
 
- ////////console.debug('Entity ancestors...ORGAN', ancestor_organ);
+ console.debug('Entity ancestors...', response.results);
  this.setState({
  source_entity: response.results[0],
  ancestor_organ: response.results[0].organ // use "top" ancestor organ