Default to one experiment visible, enable multi-experiment choices through URL

.build-files/docker-compose-local.template.yml

@@ -41,4 +41,4 @@ services:
 
 volumes:
   duckdb-data:
-  migrations_volume:
+  migrations_volume:

README.md

@@ -54,6 +54,30 @@ In the root of the repository, run the following following command:
 python3 build.py --prepare-dev
 ```
 
+### Prepare Development Environment and Run Separately with Experiment Visibility Control
+
+Experiment visibility control allows users to control which experiments are visible to them. You specify which experiments are visible to users in the `aa_index.json` file.
+
+```bash
+python3 build.py --prepare-dev --experiment-visibility-control
+```
+
+Experiment visibility control example:
+
+```json
+{
+  "experiments": [
+    {
+      "filename": "Data Discovery - Automated Cell Lineage Tracking.json",
+      "visible-by-default": true
+    },
+    "Quality Control - Cancer Triggering Microenvironments.json",
+    "Communication - Tumorigenic Cell States.json"
+  ]
+}
+```
+
+
 This will generate the necessary environment file in the client directory while still running the rest of the container. Then, the development server can be started separately by the following:
 
 ```bash
@@ -109,6 +133,7 @@ The build script will do its best to validate the config before starting the doc
 | -o, --overwrite       | When set, any settings in your configuration file which are present as environment variables in the current session will be overwritten.         | -o                             |
 | -s, --disable-spinner | When set, disables inline spinner                                                                                                                | -s                             |
 | --prepare-dev         | When set, will create the `.env` file based on the current configuration that is required to run a separate client development server.           | --prepare-dev                  |
+| --experiment-visibility-control | When set, will create the `.env` file based on the current configuration that is required to run a separate client development server. | --experiment-visibility-control|
 
 In the repository, you will see two docker directories: `docker` and `docker-local`. The main deployment will use the `docker` directory. The `docker-local` directory is a separate local version of Loon which we will discuss shortly. Below are some examples.
 

apps/client/src/stores/dataStores/datasetSelectionUntrrackedStore.ts

@@ -1,6 +1,7 @@
 import { ref, computed, watch } from 'vue';
 import { defineStore } from 'pinia';
 import { asyncComputed } from '@vueuse/core';
+import { useRoute } from 'vue-router';
 import * as vg from '@uwdata/vgplot';
 
 import { computedAsync } from '@vueuse/core';
@@ -44,7 +45,7 @@ export interface LocationMetadata {
     imageDataFilename?: string;
     segmentationsFolder?: string;
     tags?: Tags;
-    // name?: string; // user friendly name
+    name?: string; // user friendly name
     // condition?: string; // experimental condition // TODO: - does this need to be an array
     // plate?: string;
     // well?: string;
@@ -95,8 +96,9 @@ export const useDatasetSelectionStore = defineStore(
         })
 
         // Generate Experiment List
+        const route = useRoute();
         const experimentFilenameList = asyncComputed<string[]>(async () => {
-            if (configStore.serverUrl == null) return null;
+            if (configStore.serverUrl == null) return [];
             const fullURL = configStore.getFileUrl(
                 configStore.entryPointFilename
             );
@@ -115,12 +117,12 @@ export const useDatasetSelectionStore = defineStore(
                     `Could not access ${fullURL}. "${error.message}"`
                 );
             });
-            if (response == null) return;
+            if (response == null) return [];
             if (!response.ok) {
                 handleFetchEntryError(
                     `Server Error. "${response.status}: ${response.statusText}"`
                 );
-                return;
+                return [];
             }
             fetchingEntryFile.value = false;
             serverUrlValid.value = true;
@@ -136,7 +138,33 @@ export const useDatasetSelectionStore = defineStore(
             vg.coordinator().databaseConnector(connector);
 
             const data = await response.json();
-            return data.experiments;
+            const rawExperiments: (string | { filename: string; 'visible-by-default'?: boolean })[] = data.experiments;
+
+            // Normalize entries: extract filename from objects, pass strings through
+            const allFilenames = rawExperiments.map((entry) =>
+                typeof entry === 'string' ? entry : entry.filename
+            );
+
+            // If experiment visibility control is not enabled, show all experiments
+            const visibilityControlEnabled =
+                import.meta.env.VITE_EXPERIMENT_VISIBILITY_CONTROL === 'true';
+            if (!visibilityControlEnabled) {
+                return allFilenames;
+            }
+
+            // If show-all-experiments URL param is present, show all
+            if ('show-all-experiments' in route.query) {
+                return allFilenames;
+            }
+
+            // Filter to only visible-by-default experiments
+            return rawExperiments
+                .filter((entry) =>
+                    typeof entry === 'object' && entry['visible-by-default'] === true
+                )
+                .map((entry) =>
+                    typeof entry === 'string' ? entry : entry.filename
+                );
         }, [refreshTime.value]);
 
         // Sets location Metadata
@@ -284,7 +312,7 @@ export const useDatasetSelectionStore = defineStore(
                     .locationMetadataList) {
                     if (
                         datasetSelectionTrrackedStore.selectedLocationIds[
-                            location.id
+                        location.id
                         ]
                     ) {
                         return location;

build.py

@@ -81,7 +81,7 @@ def createComposeFile(local=False, nfs=False):
     shutil.copy(docker_compose_template, '.build-files/docker-compose.yml')
 
 
-def createEnvFile(configFileName, envFileName, useDid=False):
+def createEnvFile(configFileName, envFileName, useDid=False, experimentVisibilityControl=False):
     buildConfig = BuildConfig.BuildConfig(configFileName, envFileName)
     buildConfig.reportErrors()
 
@@ -110,6 +110,7 @@ def createEnvFile(configFileName, envFileName, useDid=False):
 
     buildConfig.set('VITE_ENVIRONMENT', environment)
     buildConfig.set('VITE_SERVER_URL', f'{base_url}/data')
+    buildConfig.set('VITE_EXPERIMENT_VISIBILITY_CONTROL', str(experimentVisibilityControl).lower())
 
     localPort1 = buildConfig.get("generalSettings.local_port_1")
     buildConfig.set("LOCAL_PORT_1", localPort1)
@@ -390,14 +391,16 @@ def cleanup_and_exit(signal=None, frame=None):
     sys.exit(0)
 
 
-def prepare_dev(buildConfig):
+def prepare_dev(buildConfig, experimentVisibilityControl=False):
     vite_server_url = f"{buildConfig.get('generalSettings.baseUrl')}/data"
     vite_use_http = f"{buildConfig.get('generalSettings.useHttp')}"
     vite_environment = f"{buildConfig.get('generalSettings.environment')}"
+    vite_experiment_visibility_control = str(experimentVisibilityControl).lower()
 
     outString = f"VITE_SERVER_URL={vite_server_url}\n" \
                 f"VITE_USE_HTTP={vite_use_http}\n" \
-                f"VITE_ENVIRONMENT={vite_environment}\n"
+                f"VITE_ENVIRONMENT={vite_environment}\n" \
+                f"VITE_EXPERIMENT_VISIBILITY_CONTROL={vite_experiment_visibility_control}\n"
 
     fullEnvFileName = 'apps/client/.env'
     with open(fullEnvFileName, 'w') as outF:
@@ -445,6 +448,10 @@ def spinner(msg):
                         help="Generates .env file for client environment.")
     parser.add_argument("-i", "--use-did", action="store_true", required=False,
                         help="Flag to specify that this build script is running in a DiD setup.")
+    parser.add_argument("--experiment-visibility-control", action="store_true", required=False,
+                        help="Enable experiment visibility control. Only experiments with "
+                        "'visible-by-default' in aa_index.json will be shown unless "
+                        "'show-all-experiments' URL param is used.")
 
     args = parser.parse_args()
 
@@ -464,7 +471,7 @@ def spinner(msg):
                 print('No client .env file found.')
                 pass
 
-            buildConfig = createEnvFile(config_file_name, args.env_file, args.use_did)
+            buildConfig = createEnvFile(config_file_name, args.env_file, args.use_did, args.experiment_visibility_control)
 
             use_http = buildConfig.get('generalSettings.useHttp')
             if use_http:
@@ -513,7 +520,7 @@ def spinner(msg):
             follow_all_logs(logs_path, services, args.verbose, args.detached)
 
             if args.prepare_dev:
-                prepare_dev(buildConfig)
+                prepare_dev(buildConfig, args.experiment_visibility_control)
 
             check_containers_status(services, args.detached)
         else:
@@ -522,5 +529,5 @@ def spinner(msg):
         if args.overwrite:
             config_file_name = overwrite_config(config_file_name)
 
-        buildConfig = createEnvFile(config_file_name, args.env_file, args.use_did)
+        buildConfig = createEnvFile(config_file_name, args.env_file, args.use_did, args.experiment_visibility_control)
         createComposeFile(local=buildConfig.local, nfs=buildConfig.nfs)