Merge pull request #213 from AuScope/AUS-3693

AUS-3693 Suppport GeoSciML v4.1 complex boreholes with petrophysics data

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,

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');
       }
     });
 

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) {

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);
 

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);
             }

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'),

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;

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';
@@ -21,10 +21,10 @@ export class DynamicAnalyticComponent {
   @Input() doc: QuerierInfoModel;
   private _load: boolean;
   @ViewChild('dynamicContentAnalyticPlaceholder', { read: ViewContainerRef, static: true })
-  dyanmicAnalyticHost: ViewContainerRef;
+  dynamicAnalyticHost: ViewContainerRef;
 
 
-  constructor(private componentFactoryResolver: ComponentFactoryResolver, private changeDetectorRef: ChangeDetectorRef ) { }
+  constructor(private changeDetectorRef: ChangeDetectorRef) { }
 
   @Input()
   set load(load: boolean) {
@@ -36,12 +36,11 @@ export class DynamicAnalyticComponent {
 
   loadComponent() {
 
-
-    const componentFactory = this.componentFactoryResolver.resolveComponentFactory(ref.analytic[this.layer.id]);
-
-    const viewContainerRef = this.dyanmicAnalyticHost
+    const viewContainerRef = this.dynamicAnalyticHost
     viewContainerRef.clear();
-    const componentRef = viewContainerRef.createComponent(componentFactory);
+    // 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;