Merge pull request #479 from plantinformatics/develop

Release v3.5.0 Dataset Collections

doc/adminGuides/install_and_configure.md

@@ -95,6 +95,11 @@ for i in api database blastserver; do \
 docker logs pretzel-$stage-$i-1 >& ~/log/compose/$stage/$i.$logDate; done
 ```
 
+Observe Pretzel server containers created by Docker compose :
+```
+docker ps --filter="name=pretzel-$stage-api"
+```
+
 ---
 
 ### Preparing a custom Pretzel API server container image

frontend/app/components/form/api-server.js

@@ -2,12 +2,18 @@ import $ from 'jquery';
 import { inject as service } from '@ember/service';
 import Component from '@ember/component';
 
+import { datasetsReport } from '../../utils/data/datasets-csv';
+
 //------------------------------------------------------------------------------
 
 const dLog = console.debug;
 
 //------------------------------------------------------------------------------
 
+/**
+ * @param name=apiServerName
+ * @param data=apiServer
+ */
 export default Component.extend({
   apiServers: service(),
 
@@ -39,4 +45,15 @@ export default Component.extend({
     }
   },
 
+  /** Generate a CSV / TSV report of the datasets visible to this user, and
+   * export as a file download.
+   */
+  datasetsReport() {
+    const
+    fnName = 'datasetsReport',
+    apiServer = this.data,
+    datasets = apiServer.datasetsBlocks;
+    datasetsReport(datasets, apiServer.store);
+  },
+
 });

frontend/app/components/form/natural-search.js

@@ -154,7 +154,7 @@ export default class FormNaturalSearchComponent extends Component {
       blocks = datasets.map(dataset =>
         dataset?.dataset.blocks.findBy('name', chromosome))
         .filter(block => block);
-      later(() => blocks.forEach(block => this.args.loadBlock(block)));
+      later(() => blocks.forEach(block => this.args.loadBlock(block, true)));
     }
     /* or nameChr2Block() or this.datasetService.datasetsByName,
     dataset = datasets[datasetName]; */

frontend/app/components/form/select-group.hbs

@@ -1,5 +1,6 @@
 {{!-- (queue (mut selectedValue) (action @selectedGroupChanged)) --}}
-  <select onchange={{action this.selectedGroupChangedId value="target.value"}}>
+  <select multiple={{@isMultiple}}
+     onchange={{action this.selectedGroupChangedId value="target.value" preventDefault=false}}>
     {{#each @values as |optionValue|}}
       <option value={{optionValue.id}} selected={{eq @selectedValue optionValue}}>{{optionValue.name}}</option>
     {{/each}}

frontend/app/components/form/select-group.js

@@ -1,6 +1,8 @@
 import Component from '@glimmer/component';
 import { action } from '@ember/object';
 
+import { thenOrNow } from '../../utils/common/promises';
+
 // -----------------------------------------------------------------------------
 
 const dLog = console.debug;
@@ -15,7 +17,7 @@ export default class FormSelectGroupComponent extends Component {
     const fnName = 'selectedGroupChangedId';
     let
     gsP = this.args.values,
-    selectedGroup = gsP.then((gs) => {
+    selectedGroup = thenOrNow(gsP, (gs) => {
       let
       groupValue = gs.findBy('id', selectedGroupId);
       dLog(fnName, selectedGroupId, groupValue?.name, groupValue?.id, arguments, this);

frontend/app/components/form/select-multiple.hbs

@@ -0,0 +1,10 @@
+{{!-- (queue (mut selectedValue) (action @selectedGroupChanged)) --}}
+  <select multiple
+     onchange={{action this.selectedGroupChangedId value="target.value" preventDefault=false}}>
+    {{#each @values as |optionValue|}}
+      {{!-- selected seems to be not used for multiple --}}
+      <option value={{optionValue.id}} selected={{action this.selected @selectedValue optionValue}}>{{optionValue.name}}</option>
+    {{/each}}
+  </select>
+
+{{yield}}

frontend/app/components/form/select-multiple.js

@@ -0,0 +1,42 @@
+import Component from '@glimmer/component';
+
+import { action } from '@ember/object';
+
+import { thenOrNow } from '../../utils/common/promises';
+
+// -----------------------------------------------------------------------------
+
+const dLog = console.debug;
+
+// -----------------------------------------------------------------------------
+
+export default class FormSelectMultipleComponent extends Component {
+  // selectedValue;
+
+  @action
+  selectedGroupChangedId(selectedGroupId) {
+    const fnName = 'selectedGroupChangedId';
+    let
+    gsP = this.args.values,
+    selectedGroup = thenOrNow(gsP, (gs) => {
+      let
+      groupValue = gs.findBy('id', selectedGroupId);
+      dLog(fnName, selectedGroupId, groupValue?.name, groupValue?.id, arguments, this);
+      this.args.selectedGroupChanged(groupValue);
+    });
+  }
+
+  @action
+  /**
+   * @param selectedValue @selectedValue  i.e. currently selected values
+   * @param optionValue {id, name} of the selected row
+   * selected seems to be not used for multiple.
+   */
+  selected(selectedValue, optionValue) {
+    const
+    fnName = 'selected',
+    ok = selectedValue.any(s => s.id === optionValue.id);
+    dLog(fnName, ok, selectedValue, optionValue);
+    return ok;
+  }
+}

frontend/app/components/goto-feature-list.js

@@ -19,6 +19,8 @@ export default Component.extend({
   serverTabSelected : alias('controls.serverTabSelected'),
 
   matchAliases : true,
+  /** Cleared by clearResults(), set by getBlocksOfFeatures(). */
+  showResult : true,
 
   /*----------------------------------------------------------------------------*/
   actions : {
@@ -42,6 +44,7 @@ export default Component.extend({
         : this.blocksUnique(selectedFeatureNames);
       if (activeFeatureList?.empty)
         this.set('blocksOfFeatures', blocksUnique);
+      this.set('showResult', true);
     },
 
     /** not used - the requirements shifted from setting the axis brushes from
@@ -232,6 +235,41 @@ export default Component.extend({
   }),
 
   brushFeatures() {
+  },
+
+  /** Clear the displayed search results.
+   */
+  clearResults() {
+    // This hides 'Received :'
+    this.set('showResult', false);
+
+    /* Not strictly required because showResult masks display of blocksOfFeatures and aliases. */
+    this.set('blocksOfFeatures', []);
+    this.set('aliases', []);
+
+    /*	Not effective
+    this.emptyObject(this.featuresAliases.search);
+    this.emptyObject(this.featuresAliases.result);
+    */
+    this.set('featuresAliases', {search : {}, result : {}});
+
+    /** Required to clear selected features display in the graph : triangles and labels. */
+    const features = [];
+    this.set('selected.features', features);
+    this.get('selected').featureSearchResult(features);
+  },
+
+  /** Empty the given array, i.e. mutate it.
+   * To enable clearResults() to update the display, may be achieved by
+   * upgrading this component to a native class and perhaps using tracked
+   * properties, instead of mutating the the results from blocksUnique() :
+   * blocksOfFeatures, aliases, featuresAliases,
+   */
+  emptyArray(array) {
+    for (let i = array.length; --i >= 0; ) { array.shiftObject();}
+  },
+  emptyObject(object) {
+    Object.keys(object).forEach(key => delete object[key]);
   }
 
 });

frontend/app/components/matrix-view.js

@@ -1958,7 +1958,7 @@ export default Component.extend({
     let table = this.get('table');
     let data = this.get('data');
     const gtPlainRender = this.urlOptions.gtPlainRender;
-    dLog('matrix-view', fnName, t, rows.length, rowHeaderWidth, 'colHeaderHeight', colHeaderHeight, tableHeight, table, data, this.blockSamples && 'vcf');
+    dLog('matrix-view', fnName, t, rows.length, rowHeaderWidth, 'colHeaderHeight', colHeaderHeight, tableHeight, /*table,*/ data, this.blockSamples && 'vcf');
     d3.select('body').style('--matrixViewColumnHeaderHeight', '' + colHeaderHeight + 'px');
 
     if (gtPlainRender & 0b10000) {

frontend/app/components/panel/filter-groups.js

@@ -27,7 +27,7 @@ export default Component.extend({
 
   addFilterOrGroup() {
     let data = this.get('data'),
-    filterGroup = this.get('store').createRecord('filter-Group');
+    filterGroup = this.get('store').createRecord('filter-group');
     data.pushObject(filterGroup);
   },