Merge pull request #942 from OpenSourceBrain/release/0.8.0

Release/0.8.0

.github/workflows/deploy-dev.yaml

@@ -0,0 +1,46 @@
+name: Build and Deploy OSBv2 to Dev
+on:
+  push:
+    branches: [ develop, release/* ]
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: actions/checkout@v2
+      name: Post main clone
+      with:
+        name: MetaCell/cloud-harness 
+        ref: ${{ vars.CLOUDHARNESS_BRANCH || 'master'  }}
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.9' 
+    - name: Prepare helm chart 
+      run: |
+        bash cloud-harness/install.sh
+        harness-deployment cloud-harness . -d ${{vars.DOMAIN}} -r ${{vars.REGISTRY}} -rs ${{secrets.REGISTRY_SECRET}}
+        -n ${{vars.NAMESPACE}} --write-env -e dev -i osb-portal
+    - uses: actions/upload-artifact@v4
+      with:
+          name: env_vars_to_export
+          path: deployment/.env
+  build-base-images:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Build the Docker image
+      run: |
+        cd applications/nwb-explorer
+        docker build -t mynwbexplorer -f Dockerfile --no-cache .
+    - name: Deploy to Dev
+      uses: MetaCell/deploy-osbv2@v1
+      with:
+        environment: dev
+        service: nwbexplorer
+        port: 80
+        dependencies: jupyterhub
+        git:
+

applications/common/deploy/values.yaml

@@ -1,4 +1,4 @@
 harness:
   env:
   - name: SENTRY_DSN
-    value: https://fc2326dc50e34ac2b7188130e173f002@sentry.metacell.us/5
+    value: https://fc2326dc50e34ac2b7188130e173f002@o4506739169951744.ingest.us.sentry.io/4506758817382400

applications/jupyterlab/deploy/values-quick.yaml

@@ -0,0 +1,3 @@
+harness:
+  deployment:
+    image: gcr.io/metacellllc/osb/netpyne:0.7.6.2  

applications/netpyne/Dockerfile

@@ -1,4 +1,4 @@
-FROM gcr.io/metacellllc/netpyne-ui:1.1.0
+FROM gcr.io/metacellllc/netpyne-ui:1.1.1
 
 COPY overrides/requirements.txt overrides/requirements.txt
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\

applications/netpyne/deploy/values-quick.yaml

@@ -0,0 +1,3 @@
+harness:
+  deployment:
+    image: gcr.io/metacellllc/osb/netpyne:0.7.6.2  

applications/netpyne/deploy/values.yaml

@@ -6,7 +6,6 @@ harness:
     name: proxy-public
   deployment:
     auto: false
-    image: netpyne:latest  
   jupyterhub:
     args: ["--NotebookApp.default_url=/geppetto", "--library=netpyne_ui", "--NotebookApp.notebook_dir=/opt/workspace", "--NotebookApp.disable_check_xsrf=True"]
     applicationHook: "osb_jupyter.change_pod_manifest"

applications/nfsserver/deploy/values.yaml

@@ -1,3 +1,8 @@
+
+harness:
+  deployment:
+    auto: false
+    image: gcr.io/metacellllc/osb/nfsserver:0.7.6
 # nfs server pvc disk size (/exports)
 server:
-  diskSize: 120Gi
+  diskSize: 240Gi

applications/nwb-explorer/deploy/values-quick.yaml

@@ -0,0 +1,5 @@
+harness:
+  deployment:
+    image: gcr.io/metacellllc/osb/nwb-explorer:0.7.6.2  
+  dependencies: {}
+

applications/nwb-explorer/deploy/values.yaml

@@ -7,7 +7,7 @@ harness:
   dependencies:
     git:
       - url: https://github.com/MetaCell/nwb-explorer.git
-        branch_tag: development
+        branch_tag: master
   jupyterhub:
     args: ["--debug", "--NotebookApp.default_url=/geppetto", "--library=nwb_explorer", "--NotebookApp.notebook_dir=/opt/workspace"]
     applicationHook: "osb_jupyter.change_pod_manifest"

applications/osb-portal/package.json

@@ -1,6 +1,6 @@
 {
   "name": "frontend",
-  "version": "0.7.0",
+  "version": "0.8.0",
   "description": "",
   "main": "index.js",
   "scripts": {

applications/osb-portal/src/apiclient/workspaces/.openapi-generator/FILES

@@ -2,6 +2,7 @@ apis/K8sApi.ts
 apis/RestApi.ts
 apis/index.ts
 index.ts
+models/BiomodelsRepositoryResource.ts
 models/DandiRepositoryResource.ts
 models/DownloadResource.ts
 models/FigshareRepositoryResource.ts

applications/osb-portal/src/apiclient/workspaces/models/BiomodelsRepositoryResource.ts

@@ -0,0 +1,96 @@
+/* tslint:disable */
+/* eslint-disable */
+/**
+ * OSB Workspaces manager API
+ * Opensource Brain Platform - Reference Workspaces manager API
+ *
+ * The version of the OpenAPI document: 0.2.0
+ * 
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+
+import { exists, mapValues } from '../runtime';
+import {
+    RepositoryResourceBase,
+    RepositoryResourceBaseFromJSON,
+    RepositoryResourceBaseFromJSONTyped,
+    RepositoryResourceBaseToJSON,
+} from './';
+
+/**
+ * figshare repository resource
+ * @export
+ * @interface BiomodelsRepositoryResource
+ */
+export interface BiomodelsRepositoryResource {
+    /**
+     * file name
+     * @type {string}
+     * @memberof BiomodelsRepositoryResource
+     */
+    name?: string;
+    /**
+     * Download URL of the Resource
+     * @type {string}
+     * @memberof BiomodelsRepositoryResource
+     */
+    path?: string;
+    /**
+     * OSB Repository id
+     * @type {number}
+     * @memberof BiomodelsRepositoryResource
+     */
+    osbrepositoryId?: number;
+    /**
+     * File size in bytes of the RepositoryResource
+     * @type {number}
+     * @memberof BiomodelsRepositoryResource
+     */
+    size?: number;
+    /**
+     * Date/time the ReposityResource is last modified
+     * @type {Date}
+     * @memberof BiomodelsRepositoryResource
+     */
+    timestampModified?: Date;
+}
+
+export function BiomodelsRepositoryResourceFromJSON(json: any): BiomodelsRepositoryResource {
+    return BiomodelsRepositoryResourceFromJSONTyped(json, false);
+}
+
+export function BiomodelsRepositoryResourceFromJSONTyped(json: any, ignoreDiscriminator: boolean): BiomodelsRepositoryResource {
+    if ((json === undefined) || (json === null)) {
+        return json;
+    }
+    return {
+
+        'name': !exists(json, 'name') ? undefined : json['name'],
+        'path': !exists(json, 'path') ? undefined : json['path'],
+        'osbrepositoryId': !exists(json, 'osbrepository_id') ? undefined : json['osbrepository_id'],
+        'size': !exists(json, 'size') ? undefined : json['size'],
+        'timestampModified': !exists(json, 'timestamp_modified') ? undefined : (new Date(json['timestamp_modified'])),
+    };
+}
+
+export function BiomodelsRepositoryResourceToJSON(value?: BiomodelsRepositoryResource | null): any {
+    if (value === undefined) {
+        return undefined;
+    }
+    if (value === null) {
+        return null;
+    }
+    return {
+
+        'name': value.name,
+        'path': value.path,
+        'osbrepository_id': value.osbrepositoryId,
+        'size': value.size,
+        'timestamp_modified': value.timestampModified === undefined ? undefined : (value.timestampModified.toISOString()),
+    };
+}
+
+

applications/osb-portal/src/apiclient/workspaces/models/RepositoryType.ts

@@ -23,7 +23,8 @@
 export enum RepositoryType {
     Dandi = 'dandi',
     Figshare = 'figshare',
-    Github = 'github'
+    Github = 'github',
+    Biomodels = 'biomodels'
 }
 
 export function RepositoryTypeFromJSON(json: any): RepositoryType {

applications/osb-portal/src/apiclient/workspaces/models/index.ts

@@ -1,3 +1,4 @@
+export * from './BiomodelsRepositoryResource';
 export * from './DandiRepositoryResource';
 export * from './DownloadResource';
 export * from './FigshareRepositoryResource';

applications/osb-portal/src/components/common/RepositoriesWorkspacesSearchField.tsx

@@ -10,6 +10,7 @@ import SearchIcon from "@mui/icons-material/Search";
 //style
 import { bgRegular, chipTextColor } from "../../theme";
 import styled from "@mui/system/styled";
+import { debounce } from "lodash";
 
 const StyledTextField = styled(TextField)(({ theme }) => ({
   backgroundColor: bgRegular,
@@ -44,21 +45,24 @@ interface RepositoriesSearchProps {
 }
 
 export default (props: RepositoriesSearchProps) => {
+
+  const handleChange = React.useCallback(debounce((event: React.ChangeEvent<HTMLInputElement>) => {
+    // Timout improves responsiveness while typing
+    props.filterChanged(event.target.value);
+  }, 1000), []);
+
   return (
     <StyledTextField
       variant="standard"
       id="standard-start-adornment"
       fullWidth={true}
-      value={props?.value}
       sx={{
         borderRadius: props?.borderRadius
           ? `${props?.borderRadius}px`
           : "8px 0px 0px 8px",
       }}
       placeholder="Search"
-      onChange={(e) => {
-        props.filterChanged(e.target.value.toLowerCase());
-      }}
+      onChange={handleChange}
       InputProps={{
         startAdornment: (
           <InputAdornment position="start">

applications/osb-portal/src/components/common/SearchFilterReposWorkspaces.tsx

@@ -181,9 +181,14 @@ export const SearchFilterReposWorkspaces = (
         }
       );
     }, 500),
-    []
-  );
+    [] );
 
+  const  handleTagsChange = React.useCallback((event, value) => props?.setSearchFilterValues({
+      ...props?.searchFilterValues,
+      tags: value,
+    })
+  , [props?.searchFilterValues]);
+
   return (
     <>
       <RepositoriesWorkspacesSearchField value={props.searchFilterValues.text} filterChanged={props?.filterChanged} />
@@ -223,12 +228,7 @@ export const SearchFilterReposWorkspaces = (
           onInputChange={(event, value) => {
             handleTagInput(value);
           }}
-          onChange={(event, value) =>
-            props?.setSearchFilterValues({
-              ...props?.searchFilterValues,
-              tags: value,
-            })
-          }
+          onChange={handleTagsChange}
           onClose={(event, reason) => handleTagInput("")}
           renderTags={(value, getTagProps) =>
             value.map((option, index) => (
@@ -309,6 +309,8 @@ export const SearchFilterReposWorkspaces = (
       </StyledPopover>
     </>
   );
+
+
 };
 
 export default SearchFilterReposWorkspaces;

applications/osb-portal/src/components/repository/resources.ts

@@ -3,4 +3,5 @@ import { RepositoryType } from "../../apiclient/workspaces";
 export default {
   [RepositoryType.Dandi]: "DANDI Archive",
   [RepositoryType.Github]: "GitHub",
+  [RepositoryType.Biomodels]: "Biomodels",
 } as any;