From 0bf32148afd93a645b44dca6d81e9779e85b4300 Mon Sep 17 00:00:00 2001
From: David Sehnal <dsehnal@users.noreply.github.com>
Date: Mon, 19 Dec 2022 23:10:40 +0100
Subject: [PATCH] Viewer setting for volumes and segmentations (#673)
---
src/apps/viewer/app.ts | 4 +++-
src/extensions/volumes-and-segmentations/entry-root.ts | 6 +++---
src/extensions/volumes-and-segmentations/index.ts | 6 +++---
src/extensions/volumes-and-segmentations/volseg-api/api.ts | 4 ++--
4 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/src/apps/viewer/app.ts b/src/apps/viewer/app.ts
index 76158c575..cdc4c46de 100644
--- a/src/apps/viewer/app.ts
+++ b/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],
]
};
diff --git a/src/extensions/volumes-and-segmentations/entry-root.ts b/src/extensions/volumes-and-segmentations/entry-root.ts
index b0a63b41a..b7b83f072 100644
--- a/src/extensions/volumes-and-segmentations/entry-root.ts
+++ b/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(),
diff --git a/src/extensions/volumes-and-segmentations/index.ts b/src/extensions/volumes-and-segmentations/index.ts
index 17046dd0b..8f66d7ed1 100644
--- a/src/extensions/volumes-and-segmentations/index.ts
+++ b/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());
diff --git a/src/extensions/volumes-and-segmentations/volseg-api/api.ts b/src/extensions/volumes-and-segmentations/volseg-api/api.ts
index c1be88335..930df54e8 100644
--- a/src/extensions/volumes-and-segmentations/volseg-api/api.ts
+++ b/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
}
--
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