From d09bf7c40c842fa08172c0066ff5b7936ef9fcaf Mon Sep 17 00:00:00 2001
From: Vincent Fazio <vjf@users.noreply.github.com>
Date: Tue, 29 Nov 2022 16:55:45 +1100
Subject: [PATCH 1/2] AUS-3693 Suppport GeoSciML v4.1 complex boreholes with
 petrophysics data

---
 src/app/app.module.ts                         |   3 +-
 .../downloadpanel/downloadpanel.component.ts  |   2 +-
 .../mscl/mscl.analytic.component.ts           |   9 +-
 .../layeranalytic/mscl/mscl.service.ts        |  96 +++++++++++++++-
 .../customanalytic/mscl/mscl.component.ts     |  20 +++-
 .../querier/dynamic.analytic.component.ts     |   9 +-
 .../querier/querier.modal.component.html      |  20 ++--
 .../querier/querier.modal.component.ts        | 106 ++++++++++--------
 src/environments/config.ts                    |   4 +-
 src/environments/ref.ts                       |   3 +-
 10 files changed, 195 insertions(+), 77 deletions(-)

diff --git a/src/app/app.module.ts b/src/app/app.module.ts
index 225f1d077..a763ef295 100644
--- a/src/app/app.module.ts
+++ b/src/app/app.module.ts
@@ -60,6 +60,7 @@ import { BrowserAnimationsModule } from '@angular/platform-browser/animations';
 import { BsDropdownModule } from 'ngx-bootstrap/dropdown';
 import { MSCLComponent } from './modalwindow/querier/customanalytic/mscl/mscl.component';
 import { MSCLAnalyticComponent } from './modalwindow/layeranalytic/mscl/mscl.analytic.component';
+import { MSCLService } from './modalwindow/layeranalytic/mscl/mscl.service';
 
 import { HelpMenuComponent } from './toppanel/help-menu/help-menu.component';
 
@@ -133,7 +134,7 @@ PlotlyModule.plotlyjs = PlotlyJS;
         DataExplorerComponent,
         RecordModalComponent
     ],
-    providers: [ AuscopeApiService, FilterService, RectanglesEditorService, AdvancedComponentService, SearchService, NVCLService, GraceService, {provide: SAVER, useFactory: getSaver} ],
+    providers: [ AuscopeApiService, FilterService, RectanglesEditorService, AdvancedComponentService, SearchService, NVCLService, MSCLService, GraceService, {provide: SAVER, useFactory: getSaver} ],
     imports: [
         PortalCoreModule.forRoot(environment, config),
         PortalCorePipesModule,
diff --git a/src/app/menupanel/common/downloadpanel/downloadpanel.component.ts b/src/app/menupanel/common/downloadpanel/downloadpanel.component.ts
index 8495b00e9..c25471e01 100644
--- a/src/app/menupanel/common/downloadpanel/downloadpanel.component.ts
+++ b/src/app/menupanel/common/downloadpanel/downloadpanel.component.ts
@@ -720,7 +720,7 @@ export class DownloadPanelComponent implements OnInit {
       if (UtilitiesService.isEmpty(err.message)) {
         alert('An error has occurred whilst attempting to download. Please contact cg-admin@csiro.au');
       } else {
-        alert('An error has occurred whilst attempting to download (' + err.message + '). Plese contact cg-admin@csiro.au');
+        alert('An error has occurred whilst attempting to download (' + err.message + '). Please contact cg-admin@csiro.au');
       }
     });
 
diff --git a/src/app/modalwindow/layeranalytic/mscl/mscl.analytic.component.ts b/src/app/modalwindow/layeranalytic/mscl/mscl.analytic.component.ts
index c17c0bc37..531a2c643 100644
--- a/src/app/modalwindow/layeranalytic/mscl/mscl.analytic.component.ts
+++ b/src/app/modalwindow/layeranalytic/mscl/mscl.analytic.component.ts
@@ -15,6 +15,7 @@ export class MSCLAnalyticComponent implements OnInit {
     featureId: string;  // Identifier of the borehole
     metricList: string[];  // List of metric enums to plot
     closeGraphModal: () => null;  // Function to call when the modal dialogue must be closed
+    usesGMLObs: boolean; // Response has values nested within GeoSciML observations
     serviceUrl: string; // URL of MSCL service
     processingData = false;
 
@@ -42,7 +43,7 @@ export class MSCLAnalyticComponent implements OnInit {
         const error_display = this.error_display.nativeElement;
         // Fetch data from MSCL service
         this.processingData = true;
-        this.msclService.getMSCLDownload(this.serviceUrl, this.featureId, this.startDepth, this.endDepth, this.metricList).subscribe(valuesList => {
+        this.msclService.getMSCLDownload(this.serviceUrl, this.featureId, this.startDepth, this.endDepth, this.usesGMLObs, this.metricList).subscribe(valuesList => {
             // Check response
             if (valuesList == null || !(Symbol.iterator in Object(valuesList))) {
                 this.processingData = false;
@@ -60,7 +61,11 @@ export class MSCLAnalyticComponent implements OnInit {
             for (const values of valuesList) {
                 for (const metricEnum of this.metricList) {
                     const featName = this.msclService.getMetricInfoAttr(metricEnum, 'feat_elem');
-                    xLists[metricEnum].push(values[featName]);
+                    if (this.usesGMLObs) {
+                        xLists[metricEnum].push(values[featName.replace(/_/g, ' ')]);
+                    } else {
+                        xLists[metricEnum].push(values[featName]);
+                    }
                 }
                 yList.push(values.depth);
             }
diff --git a/src/app/modalwindow/layeranalytic/mscl/mscl.service.ts b/src/app/modalwindow/layeranalytic/mscl/mscl.service.ts
index f9276d43d..37f513499 100644
--- a/src/app/modalwindow/layeranalytic/mscl/mscl.service.ts
+++ b/src/app/modalwindow/layeranalytic/mscl/mscl.service.ts
@@ -5,6 +5,7 @@ import { Injectable } from '@angular/core';
 import { HttpClient, HttpParams, HttpHeaders, HttpResponse } from '@angular/common/http';
 import { environment } from '../../../../environments/environment';
 import { Layout, Data } from 'plotly.js-dist-min';
+import { SimpleXMLService } from '@auscope/portal-core-ui';
 
 // Elements detectable via XRF
 const XRFElem = ['Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'As', 'Se', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo',
@@ -20,6 +21,7 @@ export enum Metric { diameter = "diameter",
             pWaveAmp = "pWaveAmp",
             pWaveVel = "pWaveVel",
             density = "density",
+            specificGravity = "specificGravity",
             magSuscPoint = "magSuscPoint",
             magSuscLoopVC = "magSuscLoopVC",
             magSuscLoopDC = "magSuscLoopDC",
@@ -61,6 +63,7 @@ let metricMap: Map<string, Info> = new Map( [
     [ Metric.pWaveVel, { pname: 'P-Wave Vel.', group: 'P-Wave', desc: 'P-Wave Velocity', units: 'm/s', feat_elem: 'p_wave_velocity'}],
     [ Metric.pWaveAmp, { pname: 'P-Wave Amp.', group: 'P-Wave', desc: 'P-Wave Amplitude', units: '', feat_elem: 'p_wave_amplitude'}],
     [ Metric.density,  { pname: 'Density', group: '', desc: 'Density', units: '', feat_elem: 'density'} ],
+    [ Metric.specificGravity, { pname: 'Specific Gravity', group: '', desc: 'Specfic Gravity', units: '', feat_elem: 'specific_gravity'} ],
     [ Metric.magSuscPoint, { pname: 'Mag. Susc. Point', group: '', desc: 'Magnetic Susceptibility Point', units: 'SI x 10^-5', feat_elem: 'magnetic_susc_point'}  ],
     [ Metric.magSuscLoopVC, { pname: 'Mag. Susc. LoopVC', group: '', desc: 'Magnetic Susceptibility Loop Volume Corrected', units: 'SI x 10^-5', feat_elem: 'magnetic_susceptibility'}  ],
     [ Metric.magSuscLoopDC, { pname: 'Mag. Susc. LoopDC', group: '', desc: 'Magnetic Susceptibility Loop Density Corrected', units: 'SI x 10^-5', feat_elem: 'magnetic_susc_loop_dc'}  ],
@@ -134,7 +137,7 @@ export class MSCLService {
             // Convert feature name list to a list of names and group names
             for (let featElem of featList) {
                 for (let mm of metricMap.values()) {
-                    if (mm.feat_elem === featElem) {
+                    if (mm.feat_elem === featElem.replace(/ /g, '_')) {
                         if (!retList.includes(mm.pname)) {
                             retList.push(mm.pname);
                         }
@@ -441,6 +444,83 @@ export class MSCLService {
         return traceList;
     }
 
+    /**
+    * Checks to see if there are petrophysics observation sample values
+    * Assumes GeoSciML v4.1 WFS response format
+    *
+    * @param XML string WFS response
+    * @returns true if values could be found
+    */
+    public usesGMLObs(xmlStr: string): boolean {
+        const obsIdx = xmlStr.search(/<om:OM_Observation (gml:)?id="om.observation.petrophysicalproperty/);
+        return (obsIdx > 0);
+    }
+
+    /**
+    * Namespace resolver for XPATH parsing of GeoSciML v4.1 WFS response
+    */
+    private nsResolver(prefix: any) {
+        switch (prefix) {
+          case 'wfs':
+            return "http://www.opengis.net/wfs";
+          case "xs":
+            return "http://www.w3.org/2001/XMLSchema";
+          case "swe":
+            return "http://www.opengis.net/swe/2.0";
+          case "sams":
+            return "http://www.opengis.net/samplingSpatial/2.0";
+          case "gsmlp":
+            return "http://xmlns.geosciml.org/geosciml-portrayal/4.0";
+          case "gml":
+            return "http://www.opengis.net/gml";
+          case "mt":
+            return "http://xmlns.geoscience.gov.au/mineraltenementml/1.0";
+          case "cit":
+            return "http://standards.iso.org/iso/19115/-3/cit/1.0";
+          case "gco2":
+            return "http://www.isotc211.org/2005/gco";
+          case "gsmlb":
+            return "http://www.opengis.net/gsml/4.1/GeoSciML-Basic";
+          case "gsml":
+            return "urn:cgi:xmlns:CGI:GeoSciML:2.0";
+          case "gsmlbh":
+            return "http://www.opengis.net/gsml/4.1/Borehole";
+          case "erl":
+            return "http://xmlns.earthresourceml.org/earthresourceml-lite/2.0";
+          case "om":
+            return "http://www.opengis.net/om/2.0";
+          case "sam":
+            return "http://www.opengis.net/sampling/2.0";
+          case "xlink":
+            return "http://www.w3.org/1999/xlink";
+          case "gmd":
+            return "http://www.isotc211.org/2005/gmd";
+          case "xsi":
+            return "http://www.w3.org/2001/XMLSchema-instance";
+        }
+        return "http://www.http://www.w3.org/2001/XMLSchema-instance.net/wcs";
+      }
+
+      /**
+       * Parses an XML WFS response to find the set of metric types available
+       * Applies only to GeoSciML v4.1
+       * 
+       * @param xmlStr WFS response
+       * @returns a list of strings or empty list if not found
+      */
+      public findMetricTypes(xmlStr: string): any[] {
+        const rootNode = SimpleXMLService.parseStringToDOM(xmlStr);
+        const METRICS = '//gsmlbh:specification/om:OM_Observation/om:result/swe:Quantity/swe:label';
+        const nodeList = SimpleXMLService.evaluateXPathNodeArray(rootNode, rootNode, METRICS, this.nsResolver);
+        const metricVals = [];
+        for (const node of nodeList) {
+            metricVals.push(node.textContent);
+        }
+        const metricSet = new Set(metricVals);
+        const uniqueMetrics = [ ... metricSet ];
+        return uniqueMetrics;
+    }
+
 
     /**
      * Contacts the MSCL data service and retrieves plot data
@@ -449,10 +529,12 @@ export class MSCLService {
      * @param boreholeHeaderId borehole identifier
      * @param startDepth retrieve plot data starting at this depth
      * @param endDepth retrieve plot data ending at this depth
+     * @param useGMLObs if true then observations are hidden in complete GeoSciML data model
      * @param metricList list of metrics for which plotting data is required
      * @return Observable for waiting on
      */
-    public getMSCLDownload(serviceUrl: string, boreholeHeaderId: string, startDepth: number, endDepth: number, metricList: string[]): Observable<any> {
+    public getMSCLDownload(serviceUrl: string, boreholeHeaderId: string, startDepth: number, endDepth: number,
+        useGMLObs: boolean, metricList: string[]): Observable<any> {
         let httpParams = new HttpParams();
         httpParams = httpParams.append('serviceUrl', serviceUrl);
         httpParams = httpParams.append('boreholeHeaderId', boreholeHeaderId);
@@ -462,15 +544,21 @@ export class MSCLService {
         for (const metric of metricList) {
             const feat_elem = this.getMetricInfoAttr(metric, 'feat_elem');
             if (feat_elem != '') {
-                httpParams = httpParams.append('observationsToReturn', feat_elem);
+                const std_feat_elem = (useGMLObs) ? feat_elem.replace('_',' '): feat_elem;
+                httpParams = httpParams.append('observationsToReturn', std_feat_elem);
             // If user requested a group name, append all members of group
             } else if (this.isMetricGroup(metric)) {
                 const gMetricList = this.getInfoAttrsForGrp(metric, 'feat_elem');
                 for (let gMet of gMetricList) {
-                    httpParams = httpParams.append('observationsToReturn', gMet);
+                    const cleanMetric = (useGMLObs) ? gMet.replace('_',' '): gMet;
+                    httpParams = httpParams.append('observationsToReturn', cleanMetric);
                 }
             }
         }
+        // Observations are hidden in complete GeoSciML data model
+        if (useGMLObs) {
+            httpParams = httpParams.append('useGMLObs', 'true');
+        }
         // Send HTTP request for observations for a borehole
         return this.http.post(environment.portalBaseUrl + 'getMsclObservationsForGraph.do', httpParams.toString(), {
             headers: new HttpHeaders().set('Content-Type', 'application/x-www-form-urlencoded'),
diff --git a/src/app/modalwindow/querier/customanalytic/mscl/mscl.component.ts b/src/app/modalwindow/querier/customanalytic/mscl/mscl.component.ts
index a453ddfea..8831143c1 100644
--- a/src/app/modalwindow/querier/customanalytic/mscl/mscl.component.ts
+++ b/src/app/modalwindow/querier/customanalytic/mscl/mscl.component.ts
@@ -29,6 +29,7 @@ export class MSCLComponent implements OnInit {
     public allTicked = false; // Are all tickboxes ticked?
     public showSelectMetricError: boolean; // Show error if no metrics chosen when Draw Graph is pressed
 
+    private usesGMLObs = false; // Response has values nested within GeoSciML observations
     private bsModalRef: BsModalRef;
 
     constructor(public msclService: MSCLService, private modalService: BsModalService, private changeDetectorRef: ChangeDetectorRef) {
@@ -47,9 +48,19 @@ export class MSCLComponent implements OnInit {
         // Extract the available metrics from the "datasetProperties" XML element in the WFS response
         // "datasetProperties" is a list of the metrics available in this borehole's dataset
         // The members of the list take the form of XML element names  e.g. p_wave_velocity
-        const metrics = /<gsmlp:datasetProperties>[a-z_,]*<\/gsmlp:datasetProperties>/.exec(this.doc.raw).toString();
-        // Remove tags at ends and convert to a list
-        const metricList = metrics.substring(25, metrics.length - 26).split(",");
+        let metricList = [];
+        // Find out if values are nested within GeoSciML observations
+        this.usesGMLObs = this.msclService.usesGMLObs(this.doc.raw);
+        if (this.usesGMLObs) {
+            metricList = this.msclService.findMetricTypes(this.doc.raw);
+        } else {
+            const searchResult = /<gsmlp:datasetProperties>[a-z_,]*<\/gsmlp:datasetProperties>/.exec(this.doc.raw);
+            if (searchResult) {
+                const metricsStr = searchResult.toString(); 
+                // Remove tags at ends and convert to a list
+                metricList = metricsStr.substring(25, metricsStr.length - 26).split(",");
+            }
+        }
         this.metricPNameList = this.msclService.getMetricPNameList(metricList)
 
         // Given list of metrics, set up the data structures that support tickboxes
@@ -115,7 +126,8 @@ export class MSCLComponent implements OnInit {
                     'metricList': selecMetricList,
                     'featureId': this.featureId,
                     'closeGraphModal': this.closeGraphModal.bind(this),
-                    'serviceUrl': this.onlineResource.url
+                    'serviceUrl': this.onlineResource.url,
+                    'usesGMLObs': this.usesGMLObs
                 }
             });
             this.modalDisplayed = true;
diff --git a/src/app/modalwindow/querier/dynamic.analytic.component.ts b/src/app/modalwindow/querier/dynamic.analytic.component.ts
index b3a0d6f60..9edb91dc4 100644
--- a/src/app/modalwindow/querier/dynamic.analytic.component.ts
+++ b/src/app/modalwindow/querier/dynamic.analytic.component.ts
@@ -1,7 +1,7 @@
 import { LayerModel } from '@auscope/portal-core-ui';
 import { OnlineResourceModel } from '@auscope/portal-core-ui';
 import { NVCLDatasetListComponent } from './customanalytic/nvcl/nvcl.datasetlist.component';
-import { Component, Input, ViewChild, ComponentFactoryResolver, ViewContainerRef, ChangeDetectorRef } from '@angular/core';
+import { Component, Input, ViewChild, ViewContainerRef, ChangeDetectorRef } from '@angular/core';
 import {ref} from '../../../environments/ref';
 import { QuerierInfoModel } from '@auscope/portal-core-ui';
 import { RemanentAnomaliesComponent } from './customanalytic/RemanentAnomalies/remanentanomalies.component';
@@ -24,7 +24,7 @@ export class DynamicAnalyticComponent {
   dyanmicAnalyticHost: ViewContainerRef;
 
 
-  constructor(private componentFactoryResolver: ComponentFactoryResolver, private changeDetectorRef: ChangeDetectorRef ) { }
+  constructor(private changeDetectorRef: ChangeDetectorRef) { }
 
   @Input()
   set load(load: boolean) {
@@ -36,12 +36,9 @@ export class DynamicAnalyticComponent {
 
   loadComponent() {
 
-
-    const componentFactory = this.componentFactoryResolver.resolveComponentFactory(ref.analytic[this.layer.id]);
-
     const viewContainerRef = this.dyanmicAnalyticHost
     viewContainerRef.clear();
-    const componentRef = viewContainerRef.createComponent(componentFactory);
+    const componentRef = viewContainerRef.createComponent(ref.analytic[this.layer.id]);
 
     (<NVCLDatasetListComponent>componentRef.instance).layer = this.layer;
     (<NVCLDatasetListComponent>componentRef.instance).onlineResource = this.onlineResource;
diff --git a/src/app/modalwindow/querier/querier.modal.component.html b/src/app/modalwindow/querier/querier.modal.component.html
index e0149c5a1..8e686bf5f 100644
--- a/src/app/modalwindow/querier/querier.modal.component.html
+++ b/src/app/modalwindow/querier/querier.modal.component.html
@@ -43,7 +43,7 @@ <h4 class="card-title">
 							<div class="card-header">
 								<ul id="querier-card-tab" class="nav nav-tabs float-right">
 									<li (click)="doc.home=true;doc.analytic=false;onDataChange()" [ngClass]="{'active':doc.home}"><a href="#{{doc.key}}-card-tab-home" data-toggle="tab"><i class="fa fa-list"></i><span class="d-none d-md-inline"> WFS</span></a></li>
-									<li (click)="doc.home=false;doc.analytic=true;onDataChange()" [ngClass]="{'active':doc.analytic}" title="Show analytic" *ngIf="(isNVCL(doc.layer.id) && flagAnalytic || !isNVCL(doc.layer.id)) && analyticMap[doc.layer.id]" ><a href="#{{doc.key}}-card-tab-profile" data-toggle="tab"><i class="fa fa-line-chart"></i><span class="d-none d-md-inline">&nbsp;Analytic</span></a></li>
+									<li (click)="doc.home=false;doc.analytic=true;onDataChange()" [ngClass]="{'active':doc.analytic}" title="Show analytic" *ngIf="(isNVCL(doc.layer.id) && flagAnalytic || !isNVCL(doc.layer.id)) && analyticMap[doc.layer.id] || hasMsclAnalytics" ><a href="#{{doc.key}}-card-tab-profile" data-toggle="tab"><i class="fa fa-line-chart"></i><span class="d-none d-md-inline">&nbsp;Analytic</span></a></li>
 								</ul>
 								<h4 *ngIf="doc.home" class="card-title">Feature Detail</h4>
 								<h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
@@ -64,10 +64,11 @@ <h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
 									<!-- Show HTML if XML is transformed -->
 									<div *ngIf="doc.transformed" [innerHtml]="doc.transformed"></div>
 									<!-- Show default XML Tree if there is no HTML transformation -->
-									<mat-tree *ngIf="nestedDataSource[doc.key]" [dataSource]="nestedDataSource[doc.key]" [treeControl]="nestedTreeControl[doc.key]"
+									<mat-tree *ngIf="flatTreeDataSource[doc.key]" [dataSource]="flatTreeDataSource[doc.key]" [treeControl]="flatTreeControl[doc.key]"
 										class="example-tree">
 										<dl>
-											<mat-tree-node *matTreeNodeDef="let node" style="font-size: 12px !important;padding: 3px; min-height: 0px">
+											<!-- Node without children -->
+											<mat-tree-node *matTreeNodeDef="let node" style="font-size: 12px !important; min-height: 0px"  [matTreeNodePaddingIndent]="15" matTreeNodePadding>
 												<dt style="flex: auto;">{{node.filename}}</dt>
 												<dd>{{node.type}}
 													<a *ngIf="node.type && node.type.toString().startsWith('http')" target="_blank" href="{{node.type}}">
@@ -75,19 +76,20 @@ <h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
 													</a>
 												</dd>
 											</mat-tree-node>
-											<mat-nested-tree-node *matTreeNodeDef="let node; when: hasNestedChild">
-												<dt style="flex: auto;">
-													<button mat-icon-button matTreeNodeToggle [attr.aria-label]="'toggle ' + node.filename">
+											<!-- Node with children -->
+											<mat-tree-node *matTreeNodeDef="let node; when: hasChild"  [matTreeNodePaddingIndent]="15" matTreeNodePadding>
+												<dt style="flex: auto; font-size: 12px !important">
+													<button mat-icon-button matTreeNodeToggle [matTreeNodeToggleRecursive]="true" [attr.aria-label]="'toggle ' + node.filename">
 														<mat-icon class="mat-icon-rtl-mirror">
-															{{nestedTreeControl[doc.key].isExpanded(node) ? 'expand_more' : 'chevron_right'}}
+															{{flatTreeControl[doc.key].isExpanded(node) ? 'expand_more' : 'chevron_right'}}
 														</mat-icon>
 													</button>{{node.filename}}</dt>
 												<dd>
-													<dl [class.feature-tree-invisible]="!nestedTreeControl[doc.key].isExpanded(node)" style="margin-left:10px">
+													<dl [class.feature-tree-invisible]="!flatTreeControl[doc.key].isExpanded(node)" style="margin-left:10px">
 														<ng-container matTreeNodeOutlet></ng-container>
 													</dl>
 												</dd>
-											</mat-nested-tree-node>
+											</mat-tree-node>
 										</dl>
 									</mat-tree>
 
diff --git a/src/app/modalwindow/querier/querier.modal.component.ts b/src/app/modalwindow/querier/querier.modal.component.ts
index e1a0e60ac..77c97063c 100644
--- a/src/app/modalwindow/querier/querier.modal.component.ts
+++ b/src/app/modalwindow/querier/querier.modal.component.ts
@@ -2,16 +2,16 @@ import { ApplicationRef, ChangeDetectorRef, Component, Inject, OnInit } from '@a
 import { environment } from '../../../environments/environment';
 import { config } from '../../../environments/config';
 import { ref } from '../../../environments/ref';
-import { CsClipboardService, GMLParserService, ManageStateService, Polygon, QuerierInfoModel, UtilitiesService } from '@auscope/portal-core-ui';
+import { CsClipboardService, GMLParserService, ManageStateService, Polygon, QuerierInfoModel } from '@auscope/portal-core-ui';
 import { NVCLService } from './customanalytic/nvcl/nvcl.service';
 import { BsModalRef } from 'ngx-bootstrap/modal';
-import { NestedTreeControl} from '@angular/cdk/tree';
-import { MatTreeNestedDataSource } from '@angular/material/tree';
-import { BehaviorSubject, of as observableOf } from 'rxjs';
+import { FlatTreeControl } from '@angular/cdk/tree';
+import { MatTreeFlatDataSource, MatTreeFlattener} from '@angular/material/tree';
 import { HttpClient, HttpHeaders, HttpParams } from '@angular/common/http';
 import * as _ from 'lodash';
 import * as X2JS from 'x2js';
 import { DomSanitizer } from '@angular/platform-browser';
+import { MSCLService } from '../layeranalytic/mscl/mscl.service';
 
 export class FileNode {
   children: FileNode[];
@@ -19,6 +19,13 @@ export class FileNode {
   type: any;
 }
 
+/** Flat node with expandable and level information */
+interface FlatNode {
+  expandable: boolean;
+  name: string;
+  level: number;
+}
+
 @Component({
   selector: 'app-querier-modal-window',
   templateUrl: './querier.modal.component.html',
@@ -36,16 +43,30 @@ export class QuerierModalComponent  implements OnInit {
   public analyticMap;
   public tab: {};
   public bToClipboard = false;
-  public data: FileNode[][] = [];
-  dataChange: BehaviorSubject<FileNode[]>[] = [];
-
-  nestedTreeControl: NestedTreeControl<FileNode>[] = [];
-
-  nestedDataSource: MatTreeNestedDataSource<FileNode>[] = [];
+  public hasMsclAnalytics = false; // Display 'Analytics' tab to analyse GML observations
 
   // Show a message to zoom in
   public showZoomMsg: boolean = false;
 
+  /* Transforms FileNode into displayable node */
+  private _transformer = (node: FileNode, level: number) => {
+    return {
+      expandable: !!node.children && node.children.length > 0,
+      filename: node.filename,
+      type: node.type,
+      level: level,
+    };
+  };
+
+  // Data Structures used to create a folding flat tree which displays feature data
+  public flatTreeControl = {};
+  public treeFlattener = new MatTreeFlattener(this._transformer, node => node.level, node => node.expandable, node => node.children);
+  public flatTreeDataSource = {}; // Tree structure is assigned to this
+
+  // Does the 'FlatNode' have children?
+  public hasChild = (_: number, node: FlatNode) => node.expandable;
+
+
   /**
    * 
    * Reflects the value of nvclService.getAnalytic(); updates the html Analytic TAB
@@ -65,8 +86,10 @@ export class QuerierModalComponent  implements OnInit {
   constructor(public nvclService: NVCLService, public bsModalRef: BsModalRef, public csClipboardService: CsClipboardService,
         private manageStateService: ManageStateService, private gmlParserService: GMLParserService,
         private http: HttpClient, @Inject('env') private env, private sanitizer: DomSanitizer,
-        private changeDetectorRef: ChangeDetectorRef, private appRef: ApplicationRef) {
+        private changeDetectorRef: ChangeDetectorRef, private appRef: ApplicationRef,
+        private msclService: MSCLService) {
     this.analyticMap = ref.analytic;
+    this.flagAnalytic = false;
   }
 
   ngOnInit() {
@@ -79,6 +102,7 @@ export class QuerierModalComponent  implements OnInit {
       // console.log("[querier]ngOnInit().getAnalytic() = "+result);
       this.flagAnalytic = result;
 
+      // Calling this to update the UI
       this.onDataChange();
     });
 
@@ -87,19 +111,19 @@ export class QuerierModalComponent  implements OnInit {
   /**
    * Returns true iff layer is NVCL layer
    * 
-   * @param layer layer odentifier string
+   * @param layer layer identifier string
    * @returns true iff layer is NVCL layer
    */
   public isNVCL(layer: string): boolean {
     return this.nvclService.isNVCL(layer);
   }
 
-  public getData() {return this.data}
-
-  private _getChildren = (node: FileNode) => observableOf(node.children);
-
-  hasNestedChild = (_: number, nodeData: FileNode) =>  (nodeData.children);
-
+  /**
+   * Returns true if this supports open in new window
+   * 
+   * @param doc 
+   * @returns boolean
+   */
   public supportOpenInNewWindow(doc: QuerierInfoModel): boolean {
     return config.supportOpenInNewWindow.includes(doc.layer.id);
   }
@@ -157,13 +181,24 @@ export class QuerierModalComponent  implements OnInit {
     }
   }
 
+  // Look for changes and update UI after brief delay
   public onDataChange(): void {
     setTimeout(() => {
       this.changeDetectorRef.detectChanges();
     }, 50);
   }
 
+  /**
+   * This gets called from the UI when user clicks on first link in popup
+   * 
+   * @param document
+   */
   public transformToHtml(document): void {
+
+    if (this.msclService.usesGMLObs(document.raw)) {
+      this.hasMsclAnalytics = true;
+    }
+
     if (!document.expanded) {
       document.expanded = true;
     } else {
@@ -223,7 +258,7 @@ export class QuerierModalComponent  implements OnInit {
     const name = document.key;
     const doc = document.value;
 
-    if (this.nestedDataSource[name]) {
+    if (this.flatTreeDataSource[name]) {
       return;
     }
 
@@ -238,18 +273,6 @@ export class QuerierModalComponent  implements OnInit {
     const reg = new RegExp(config.clipboard.supportedLayersRegKeyword, 'gi');
     this.bToClipboard = name.search(reg) === -1 ? false : true;
 
-    this.nestedTreeControl[name] = new NestedTreeControl<FileNode>(this._getChildren);
-    this.nestedDataSource[name] = new MatTreeNestedDataSource();
-    this.dataChange[name] = new BehaviorSubject<FileNode[]>(this.data[name]);
-    this.dataChange[name].subscribe(data => {
-      this.nestedDataSource[name].data = data;
-      if (data !== undefined) {
-        this.nestedTreeControl[name].expandDescendants(data[0]);
-        const geomnode = this.findtheGeom(data[0]);
-        if (geomnode) { this.nestedTreeControl[name].collapse(geomnode); }
-      }
-    });
-
     let result = doc;
     // If it is not JSON then convert to JSON
     if (document.hasOwnProperty('format') && document.format !== 'JSON') {
@@ -261,24 +284,11 @@ export class QuerierModalComponent  implements OnInit {
         console.log('XML to JSON conversion error: ', e);
       }
     }
+    // Parse the response and build a recursive tree of FileNode objects and assign them to the tree
     const data = this.buildFileTree(JSON.parse(`{"${name}":${JSON.stringify(result)}}`), 0);
-    this.dataChange[name].next(data);
-    this.onDataChange();
-  }
-
-
-  /**
-   * Recursively searches for geometry elements
-   * @param Node starts search here
-   * @returns a geometry FileNode or null
-   */
-  private findtheGeom(Node: FileNode): FileNode {
-    if (Node.filename === 'the_geom' || Node.filename === 'shape' ) { return Node; }
-    for (let i = 0; Node.children && i < Node.children.length; i++) {
-      const foundnode = this.findtheGeom(Node.children[i]);
-      if (foundnode) { return foundnode }
-    }
-    return null;
+    this.flatTreeControl[name] = new FlatTreeControl<FlatNode>(node => node.level, node => node.expandable); 
+    this.flatTreeDataSource[name] = new MatTreeFlatDataSource(this.flatTreeControl[name], this.treeFlattener);
+    this.flatTreeDataSource[name].data = data;
   }
 
   /**
diff --git a/src/environments/config.ts b/src/environments/config.ts
index 8d01ab73d..50becca17 100644
--- a/src/environments/config.ts
+++ b/src/environments/config.ts
@@ -174,7 +174,8 @@ export const config = {
     'Octopus-Sahul-Sed-Archives-Fluvial-Osl',
     'Octopus-Sahul-Sed-Archives-Fluvial-Tl',
     'Octopus-Sahul-Sed-Archives-Lacustrine-Osl',
-    'Octopus-Sahul-Sed-Archives-Lacustrine-Tl'
+    'Octopus-Sahul-Sed-Archives-Lacustrine-Tl',
+    'mscl-gssa-borehole'
   ],
   // Layers that use CSW records to display a simple rectangle on map
   cswrenderer: [
@@ -229,6 +230,7 @@ export const config = {
     'tima-geosample',
     'tima-shrimp-geosample',
     'mscl-borehole',
+    'mscl-gssa-borehole',
     'pressuredb-borehole',
     'sf0-borehole-nvcl'
   ],
diff --git a/src/environments/ref.ts b/src/environments/ref.ts
index e4d646d6e..3de650083 100644
--- a/src/environments/ref.ts
+++ b/src/environments/ref.ts
@@ -17,7 +17,8 @@ export const ref = {
     'tima-geosample': TIMAComponent,
     'remanent-anomalies': RemanentAnomaliesComponent,
     'remanent-anomalies-EMAG': RemanentAnomaliesComponent,
-    'mscl-borehole': MSCLComponent
+    'mscl-borehole': MSCLComponent,
+    'mscl-gssa-borehole': MSCLComponent
   },
   layeranalytic: {
     'nvcl-v2-borehole': NVCLBoreholeAnalyticComponent

From 8663054506615f4718ef5eb1d5b5db19b2e869df Mon Sep 17 00:00:00 2001
From: Vincent Fazio <vjf@users.noreply.github.com>
Date: Thu, 1 Dec 2022 13:50:23 +1100
Subject: [PATCH 2/2] AUS-3693 Enable 'Analytics' tab only when there are MSCL
 observations available

---
 .../common/filterpanel/filterpanel.component.ts   | 15 ---------------
 .../dynamic.layer.analytic.component.ts           |  4 ++--
 .../querier/dynamic.analytic.component.ts         |  8 +++++---
 .../querier/querier.modal.component.html          | 15 ++++++++-------
 .../querier/querier.modal.component.ts            | 10 ++++++----
 src/environments/ref.ts                           |  3 +--
 6 files changed, 22 insertions(+), 33 deletions(-)

diff --git a/src/app/menupanel/common/filterpanel/filterpanel.component.ts b/src/app/menupanel/common/filterpanel/filterpanel.component.ts
index ceb921b93..127883440 100644
--- a/src/app/menupanel/common/filterpanel/filterpanel.component.ts
+++ b/src/app/menupanel/common/filterpanel/filterpanel.component.ts
@@ -178,21 +178,6 @@ export class FilterPanelComponent implements OnInit {
       optionalFilters: _.cloneDeep(this.optionalFilters)
     };
 
-    // VT: append advance filter to mandatory filter.
-    /*
-    // deprecated, use AdvanceFilterDirective
-    for (const idx in this.advancedParam) {
-      if (!this.layer.filterCollection.mandatoryFilters) {
-        this.layer.filterCollection.mandatoryFilters = [];
-      }
-      this.layer.filterCollection.mandatoryFilters.push({
-        parameter: idx,
-        value: this.advancedParam[idx]
-      });
-    }
-    */
-    // VT: End append
-
     // TODO: Store time period with state
     // WMS layers may have a time set
     if (this.layerTimes.currentTime) {
diff --git a/src/app/modalwindow/layeranalytic/dynamic.layer.analytic.component.ts b/src/app/modalwindow/layeranalytic/dynamic.layer.analytic.component.ts
index 4a37ed2dd..4fd54d77e 100644
--- a/src/app/modalwindow/layeranalytic/dynamic.layer.analytic.component.ts
+++ b/src/app/modalwindow/layeranalytic/dynamic.layer.analytic.component.ts
@@ -12,7 +12,7 @@ import { LayerAnalyticInterface } from './layer.analytic.interface';
 export class DynamicLayerAnalyticComponent {
   private _layer: LayerModel;
   @ViewChild('dynamicLayerContentAnalyticPlaceholder', { read: ViewContainerRef, static: true })
-  dyanmicAnalyticHost: ViewContainerRef;
+  dynamicAnalyticHost: ViewContainerRef;
 
 
   constructor(private componentFactoryResolver: ComponentFactoryResolver, private changeDetectorRef: ChangeDetectorRef ) { }
@@ -34,7 +34,7 @@ export class DynamicLayerAnalyticComponent {
 
     const componentFactory = this.componentFactoryResolver.resolveComponentFactory(ref.layeranalytic[this._layer.id]);
 
-    const viewContainerRef = this.dyanmicAnalyticHost
+    const viewContainerRef = this.dynamicAnalyticHost
     viewContainerRef.clear();
     const componentRef = viewContainerRef.createComponent(componentFactory);
 
diff --git a/src/app/modalwindow/querier/dynamic.analytic.component.ts b/src/app/modalwindow/querier/dynamic.analytic.component.ts
index 9edb91dc4..f37d2f596 100644
--- a/src/app/modalwindow/querier/dynamic.analytic.component.ts
+++ b/src/app/modalwindow/querier/dynamic.analytic.component.ts
@@ -21,7 +21,7 @@ export class DynamicAnalyticComponent {
   @Input() doc: QuerierInfoModel;
   private _load: boolean;
   @ViewChild('dynamicContentAnalyticPlaceholder', { read: ViewContainerRef, static: true })
-  dyanmicAnalyticHost: ViewContainerRef;
+  dynamicAnalyticHost: ViewContainerRef;
 
 
   constructor(private changeDetectorRef: ChangeDetectorRef) { }
@@ -36,9 +36,11 @@ export class DynamicAnalyticComponent {
 
   loadComponent() {
 
-    const viewContainerRef = this.dyanmicAnalyticHost
+    const viewContainerRef = this.dynamicAnalyticHost
     viewContainerRef.clear();
-    const componentRef = viewContainerRef.createComponent(ref.analytic[this.layer.id]);
+    // Default to MSCLComponent
+    const component = this.layer.id in ref.analytic? ref.analytic[this.layer.id]: MSCLComponent;
+    const componentRef = viewContainerRef.createComponent(component);
 
     (<NVCLDatasetListComponent>componentRef.instance).layer = this.layer;
     (<NVCLDatasetListComponent>componentRef.instance).onlineResource = this.onlineResource;
diff --git a/src/app/modalwindow/querier/querier.modal.component.html b/src/app/modalwindow/querier/querier.modal.component.html
index 8e686bf5f..af0e8f270 100644
--- a/src/app/modalwindow/querier/querier.modal.component.html
+++ b/src/app/modalwindow/querier/querier.modal.component.html
@@ -43,7 +43,7 @@ <h4 class="card-title">
 							<div class="card-header">
 								<ul id="querier-card-tab" class="nav nav-tabs float-right">
 									<li (click)="doc.home=true;doc.analytic=false;onDataChange()" [ngClass]="{'active':doc.home}"><a href="#{{doc.key}}-card-tab-home" data-toggle="tab"><i class="fa fa-list"></i><span class="d-none d-md-inline"> WFS</span></a></li>
-									<li (click)="doc.home=false;doc.analytic=true;onDataChange()" [ngClass]="{'active':doc.analytic}" title="Show analytic" *ngIf="(isNVCL(doc.layer.id) && flagAnalytic || !isNVCL(doc.layer.id)) && analyticMap[doc.layer.id] || hasMsclAnalytics" ><a href="#{{doc.key}}-card-tab-profile" data-toggle="tab"><i class="fa fa-line-chart"></i><span class="d-none d-md-inline">&nbsp;Analytic</span></a></li>
+									<li (click)="doc.home=false;doc.analytic=true;onDataChange()" [ngClass]="{'active':doc.analytic}" title="Show analytic" *ngIf="(isNVCL(doc.layer.id) && flagNVCLAnalytic || !isNVCL(doc.layer.id)) && analyticMap[doc.layer.id] || hasMsclAnalytics" ><a href="#{{doc.key}}-card-tab-profile" data-toggle="tab"><i class="fa fa-line-chart"></i><span class="d-none d-md-inline">&nbsp;Analytic</span></a></li>
 								</ul>
 								<h4 *ngIf="doc.home" class="card-title">Feature Detail</h4>
 								<h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
@@ -53,6 +53,7 @@ <h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
 							<!-- BEGIN tab-content -->
 							<div id="card-tab-content" class="tab-content" style="max-height:calc(75vh)">
 								<!-- BEGIN tab-pane -->
+								<!-- Content of WFS Tab -->
 								<div *ngIf="doc.key !== 'Server Error'" class="tab-pane fade" [ngClass]="{'active show':doc.home}" id="{{doc.key}}-card-tab-home">
 									<div *ngIf="bToClipboard || supportOpenInNewWindow(doc)" style="position: inherit;padding-top: unset;margin-bottom: 20px;">
 										<div class="float-left d-none d-md-inline mt-0 w-100">
@@ -64,11 +65,10 @@ <h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
 									<!-- Show HTML if XML is transformed -->
 									<div *ngIf="doc.transformed" [innerHtml]="doc.transformed"></div>
 									<!-- Show default XML Tree if there is no HTML transformation -->
-									<mat-tree *ngIf="flatTreeDataSource[doc.key]" [dataSource]="flatTreeDataSource[doc.key]" [treeControl]="flatTreeControl[doc.key]"
-										class="example-tree">
+									<mat-tree *ngIf="flatTreeDataSource[doc.key]" [dataSource]="flatTreeDataSource[doc.key]" [treeControl]="flatTreeControl[doc.key]">
 										<dl>
 											<!-- Node without children -->
-											<mat-tree-node *matTreeNodeDef="let node" style="font-size: 12px !important; min-height: 0px"  [matTreeNodePaddingIndent]="15" matTreeNodePadding>
+											<mat-tree-node *matTreeNodeDef="let node" style="font-size: 12px !important; min-height: 0px"  [matTreeNodePaddingIndent]="10" matTreeNodePadding>
 												<dt style="flex: auto;">{{node.filename}}</dt>
 												<dd>{{node.type}}
 													<a *ngIf="node.type && node.type.toString().startsWith('http')" target="_blank" href="{{node.type}}">
@@ -77,7 +77,7 @@ <h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
 												</dd>
 											</mat-tree-node>
 											<!-- Node with children -->
-											<mat-tree-node *matTreeNodeDef="let node; when: hasChild"  [matTreeNodePaddingIndent]="15" matTreeNodePadding>
+											<mat-tree-node *matTreeNodeDef="let node; when: hasChild" [matTreeNodePaddingIndent]="10" matTreeNodePadding>
 												<dt style="flex: auto; font-size: 12px !important">
 													<button mat-icon-button matTreeNodeToggle [matTreeNodeToggleRecursive]="true" [attr.aria-label]="'toggle ' + node.filename">
 														<mat-icon class="mat-icon-rtl-mirror">
@@ -98,10 +98,11 @@ <h4 *ngIf="doc.analytic" class="card-title">Analytic</h4>
 								<div *ngIf="doc.key === 'Server Error'" class="tab-pane fade" [ngClass]="{'active show':doc.home}" id="{{doc.key}}-card-tab-home">
 									<p>Sorry - {{doc.onlineResource.url}} server has returned an error message. See browser console for more information</p>
 								</div>
-
 								<!-- END tab-pane -->
+
 								<!-- BEGIN tab-pane -->
-								<div *ngIf="analyticMap[doc.layer.id]" class="tab-pane fade" [ngClass]="{'active show':doc.analytic}" id="{{doc.key}}-card-tab-profile">
+								<!-- Content of Analytics Tab -->
+								<div *ngIf="analyticMap[doc.layer.id] || hasMsclAnalytics" class="tab-pane fade" [ngClass]="{'active show':doc.analytic}" id="{{doc.key}}-card-tab-profile">
 									<app-custom-analytic [layer]="doc.layer" [load]="doc.loadSubComponent" [onlineResource] = "doc.onlineResource" [featureId]="doc.key" [doc] = "doc"></app-custom-analytic>
 								</div>
 								<!-- END tab-pane -->
diff --git a/src/app/modalwindow/querier/querier.modal.component.ts b/src/app/modalwindow/querier/querier.modal.component.ts
index 77c97063c..6a62dea15 100644
--- a/src/app/modalwindow/querier/querier.modal.component.ts
+++ b/src/app/modalwindow/querier/querier.modal.component.ts
@@ -81,7 +81,7 @@ export class QuerierModalComponent  implements OnInit {
    * 
    * If this was not done the two components would not see the same state of the service variable "isAnalytic"
   */
-  public flagAnalytic: boolean;
+  public flagNVCLAnalytic: boolean;
 
   constructor(public nvclService: NVCLService, public bsModalRef: BsModalRef, public csClipboardService: CsClipboardService,
         private manageStateService: ManageStateService, private gmlParserService: GMLParserService,
@@ -89,18 +89,18 @@ export class QuerierModalComponent  implements OnInit {
         private changeDetectorRef: ChangeDetectorRef, private appRef: ApplicationRef,
         private msclService: MSCLService) {
     this.analyticMap = ref.analytic;
-    this.flagAnalytic = false;
+    this.flagNVCLAnalytic = false;
   }
 
   ngOnInit() {
 
   /**
    * Checks the state of "isAnalytic" variable in the nvclService - observable
-   * and updates the local variable "flagAnalytic" - which updates the Analytic TAB in the html
+   * and updates the local variable "flagNVCLAnalytic" - which updates the Analytic TAB in the html
    */
     this.nvclService.getAnalytic().subscribe((result) => {
       // console.log("[querier]ngOnInit().getAnalytic() = "+result);
-      this.flagAnalytic = result;
+      this.flagNVCLAnalytic = result;
 
       // Calling this to update the UI
       this.onDataChange();
@@ -289,6 +289,8 @@ export class QuerierModalComponent  implements OnInit {
     this.flatTreeControl[name] = new FlatTreeControl<FlatNode>(node => node.level, node => node.expandable); 
     this.flatTreeDataSource[name] = new MatTreeFlatDataSource(this.flatTreeControl[name], this.treeFlattener);
     this.flatTreeDataSource[name].data = data;
+    this.flatTreeControl[name].expandAll();
+    this.changeDetectorRef.detectChanges();
   }
 
   /**
diff --git a/src/environments/ref.ts b/src/environments/ref.ts
index 3de650083..e4d646d6e 100644
--- a/src/environments/ref.ts
+++ b/src/environments/ref.ts
@@ -17,8 +17,7 @@ export const ref = {
     'tima-geosample': TIMAComponent,
     'remanent-anomalies': RemanentAnomaliesComponent,
     'remanent-anomalies-EMAG': RemanentAnomaliesComponent,
-    'mscl-borehole': MSCLComponent,
-    'mscl-gssa-borehole': MSCLComponent
+    'mscl-borehole': MSCLComponent
   },
   layeranalytic: {
     'nvcl-v2-borehole': NVCLBoreholeAnalyticComponent