Viewer setting for volumes and segmentations (#673)

src/apps/viewer/app.ts

@@ -9,7 +9,7 @@ import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { CellPack } from '../../extensions/cellpack';
 import { DnatcoConfalPyramids } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { Volseg } from '../../extensions/volumes-and-segmentations';
+import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
 import { GeometryExport } from '../../extensions/geo-export';
 import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
@@ -107,6 +107,7 @@ const DefaultViewerOptions = {
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default' as SaccharideCompIdMapType,
+    volumesAndSegmentationsDefaultServer: VolsegVolumeServerConfig.DefaultServer.defaultValue,
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 
@@ -181,6 +182,7 @@ export class Viewer {
                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                 [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
                 [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+                [VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
             ]
         };
 

src/extensions/volumes-and-segmentations/entry-root.ts

@@ -20,7 +20,7 @@ import { shallowEqualObjects } from '../../mol-util';
 import { ParamDefinition } from '../../mol-util/param-definition';
 import { MeshlistData } from '../meshes/mesh-extension';
 
-import { DEFAULT_VOLUME_SERVER_V2, VolumeApiV2 } from './volseg-api/api';
+import { DEFAULT_VOLSEG_SERVER, VolumeApiV2 } from './volseg-api/api';
 import { Segment } from './volseg-api/data';
 import { MetadataWrapper } from './volseg-api/utils';
 import { VolsegMeshSegmentationData } from './entry-meshes';
@@ -48,7 +48,7 @@ export type Source = Choice.Values<typeof SourceChoice>;
 
 
 export function createLoadVolsegParams(plugin?: PluginContext, entrylists: { [source: string]: string[] } = {}) {
-    const defaultVolumeServer = plugin?.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLUME_SERVER_V2;
+    const defaultVolumeServer = plugin?.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLSEG_SERVER;
     return {
         serverUrl: ParamDefinition.Text(defaultVolumeServer),
         source: ParamDefinition.Mapped(SourceChoice.values[0], SourceChoice.options, src => entryParam(entrylists[src])),
@@ -65,7 +65,7 @@ function entryParam(entries: string[] = []) {
 type LoadVolsegParamValues = ParamDefinition.Values<ReturnType<typeof createLoadVolsegParams>>;
 
 export function createVolsegEntryParams(plugin?: PluginContext) {
-    const defaultVolumeServer = plugin?.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLUME_SERVER_V2;
+    const defaultVolumeServer = plugin?.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLSEG_SERVER;
     return {
         serverUrl: ParamDefinition.Text(defaultVolumeServer),
         source: SourceChoice.PDSelect(),

src/extensions/volumes-and-segmentations/index.ts

@@ -10,7 +10,7 @@ import { PluginConfigItem } from '../../mol-plugin/config';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateAction } from '../../mol-state';
 import { Task } from '../../mol-task';
-import { DEFAULT_VOLUME_SERVER_V2, VolumeApiV2 } from './volseg-api/api';
+import { DEFAULT_VOLSEG_SERVER, VolumeApiV2 } from './volseg-api/api';
 
 import { VolsegEntryData, VolsegEntryParamValues, createLoadVolsegParams } from './entry-root';
 import { VolsegGlobalState } from './global-state';
@@ -23,7 +23,7 @@ const DEBUGGING = window.location.hostname === 'localhost';
 
 export const VolsegVolumeServerConfig = {
     // DefaultServer: new PluginConfigItem('volseg-volume-server', DEFAULT_VOLUME_SERVER_V2),
-    DefaultServer: new PluginConfigItem('volseg-volume-server', DEBUGGING ? 'http://localhost:9000/v2' : DEFAULT_VOLUME_SERVER_V2),
+    DefaultServer: new PluginConfigItem('volseg-volume-server', DEBUGGING ? 'http://localhost:9000/v2' : DEFAULT_VOLSEG_SERVER),
 };
 
 
@@ -57,7 +57,7 @@ export const Volseg = PluginBehavior.create<{ autoAttach: boolean, showTooltip:
             this.ctx.customStructureControls.delete('volseg');
         }
         private async initializeEntryLists() {
-            const apiUrl = this.ctx.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLUME_SERVER_V2;
+            const apiUrl = this.ctx.config.get(VolsegVolumeServerConfig.DefaultServer) ?? DEFAULT_VOLSEG_SERVER;
             const api = new VolumeApiV2(apiUrl);
             const entryLists = await api.getEntryList(10 ** 6);
             Object.values(entryLists).forEach(l => l.sort());

src/extensions/volumes-and-segmentations/volseg-api/api.ts

@@ -7,13 +7,13 @@
 import { type Metadata } from './data';
 
 
-export const DEFAULT_VOLUME_SERVER_V2 = 'https://molstarvolseg.ncbr.muni.cz/v2';
+export const DEFAULT_VOLSEG_SERVER = 'https://molstarvolseg.ncbr.muni.cz/v2';
 
 
 export class VolumeApiV2 {
     public volumeServerUrl: string;
 
-    public constructor(volumeServerUrl: string = DEFAULT_VOLUME_SERVER_V2) {
+    public constructor(volumeServerUrl: string = DEFAULT_VOLSEG_SERVER) {
         this.volumeServerUrl = volumeServerUrl.replace(/\/$/, ''); // trim trailing slash
     }