Merge pull request #941 from OpenSourceBrain/feature/biomodels

Feature/biomodels

.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/jupyterlab/deploy/values-quick.yaml

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

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/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/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/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;

applications/osb-portal/src/pages/RepositoryPage.tsx

@@ -257,6 +257,13 @@ export const RepositoryPage = (props: any) => {
       case "figshare":
         window.open(`${repository.uri}`, "_blank");
         break;
+      // Biomodels: repo.version
+      case "biomodels":
+        window.open(
+          `${repository.uri + "." + repository.defaultContext}`,
+          "_blank"
+        );
+        break;
       default:
         window.open(`#`, "_blank");
     }

applications/workspaces/api/openapi.yaml

@@ -993,6 +993,7 @@ components:
                 - dandi
                 - figshare
                 - github
+                - biomodels
             type: string
         RepositoryContentType:
             description: |
@@ -1412,7 +1413,6 @@ components:
                 -
                     $ref: '#/components/schemas/WorkspaceResourceBase'
                 -
-                    x-tablename: Workspaceresource
                     properties:
                         origin:
                             description: Origin data JSON formatted of the WorkspaceResource
@@ -1425,6 +1425,7 @@ components:
                             description: WorkspaceResource path where the resource will stored in the pvc.
                             type: string
                             example: repo/sample.nwb
+                    x-tablename: Workspaceresource
         WorkspaceResource:
             description: Workspace Resource item of a Workspace
             allOf:
@@ -1505,6 +1506,11 @@ components:
                                 $ref: '#/components/schemas/Tag'
                             -
                                 x-secondary: osbrepository_tag
+        BiomodelsRepositoryResource:
+            description: figshare repository resource
+            allOf:
+                -
+                    $ref: '#/components/schemas/RepositoryResourceBase'
     securitySchemes:
         bearerAuth:
             scheme: bearer
@@ -1523,4 +1529,4 @@ tags:
         description: Consumer
     -
         name: Client
-        description: Client
+        description: Client

applications/workspaces/server/.openapi-generator/FILES

@@ -5,17 +5,21 @@ workspaces/controllers/k8s_controller.py
 workspaces/controllers/rest_controller.py
 workspaces/controllers/security_controller_.py
 workspaces/models/base_model_.py
+workspaces/models/biomodels_repository_resource.py
 workspaces/models/dandi_repository_resource.py
 workspaces/models/download_resource.py
 workspaces/models/figshare_repository_resource.py
 workspaces/models/git_repository_resource.py
 workspaces/models/git_repository_resource_all_of.py
+workspaces/models/inline_object.py
+workspaces/models/inline_response200.py
+workspaces/models/inline_response2001.py
+workspaces/models/inline_response2002.py
+workspaces/models/inline_response2003.py
 workspaces/models/osb_repository.py
 workspaces/models/osb_repository_all_of.py
 workspaces/models/osb_repository_base.py
-workspaces/models/osb_repository_base_tags_inner.py
 workspaces/models/osb_repository_entity.py
-workspaces/models/osbrepository_get200_response.py
 workspaces/models/pagination.py
 workspaces/models/repository_content_type.py
 workspaces/models/repository_info.py
@@ -29,27 +33,21 @@ workspaces/models/resource_origin.py
 workspaces/models/resource_status.py
 workspaces/models/resource_type.py
 workspaces/models/tag.py
-workspaces/models/tag_get200_response.py
 workspaces/models/user.py
 workspaces/models/valid.py
 workspaces/models/volume_storage.py
-workspaces/models/volumestorage_get200_response.py
 workspaces/models/workspace.py
 workspaces/models/workspace_all_of.py
 workspaces/models/workspace_base.py
-workspaces/models/workspace_base_gallery_inner.py
-workspaces/models/workspace_base_tags_inner.py
 workspaces/models/workspace_collaborator.py
 workspaces/models/workspace_entity.py
 workspaces/models/workspace_entity_all_of.py
-workspaces/models/workspace_get200_response.py
 workspaces/models/workspace_image.py
 workspaces/models/workspace_resource.py
 workspaces/models/workspace_resource_all_of.py
 workspaces/models/workspace_resource_base.py
 workspaces/models/workspace_resource_entity.py
 workspaces/models/workspace_resource_entity_all_of.py
-workspaces/models/workspaces_controllers_workspace_controller_import_resources_request.py
 workspaces/openapi/openapi.yaml
 workspaces/typing_utils.py
 workspaces/util.py

applications/workspaces/server/.openapi-generator/VERSION

@@ -1 +1 @@
-6.2.1
+5.1.0

applications/workspaces/server/README.md

@@ -8,7 +8,7 @@ is an example of building a OpenAPI-enabled Flask server.
 This example uses the [Connexion](https://github.com/zalando/connexion) library on top of Flask.
 
 ## Requirements
-Python 3.9+
+Python 3.5.2+
 
 ## Usage
 To run the server, please execute the following from the root directory:

applications/workspaces/server/git_push.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 # ref: https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/
 #
-# Usage example: /bin/sh ./git_push.sh wing328 openapi-petstore-perl "minor update" "gitlab.com"
+# Usage example: /bin/sh ./git_push.sh wing328 openapi-pestore-perl "minor update" "gitlab.com"
 
 git_user_id=$1
 git_repo_id=$2
@@ -38,14 +38,14 @@ git add .
 git commit -m "$release_note"
 
 # Sets the new remote
-git_remote=$(git remote)
+git_remote=`git remote`
 if [ "$git_remote" = "" ]; then # git remote not defined
 
     if [ "$GIT_TOKEN" = "" ]; then
         echo "[INFO] \$GIT_TOKEN (environment variable) is not set. Using the git credential in your environment."
         git remote add origin https://${git_host}/${git_user_id}/${git_repo_id}.git
     else
-        git remote add origin https://${git_user_id}:"${GIT_TOKEN}"@${git_host}/${git_user_id}/${git_repo_id}.git
+        git remote add origin https://${git_user_id}:${GIT_TOKEN}@${git_host}/${git_user_id}/${git_repo_id}.git
     fi
 
 fi
@@ -55,3 +55,4 @@ git pull origin master
 # Pushes (Forces) the changes in the local repository up to the remote repository
 echo "Git pushing to https://${git_host}/${git_user_id}/${git_repo_id}.git"
 git push origin master 2>&1 | grep -v 'To https'
+

applications/workspaces/server/setup.py

@@ -24,7 +24,7 @@
     "flask_cors",
     "sentry-sdk",
     "responses==0.22.0",
-    "jinja2<3.1.0"
+    "jinja2<3.2.0"
 ]
 
 setup(

applications/workspaces/server/workspaces/controllers/k8s_controller.py

@@ -1,8 +1,5 @@
 import connexion
 import six
-from typing import Dict
-from typing import Tuple
-from typing import Union
 
 from workspaces import util
 
@@ -13,7 +10,7 @@ def live():  # noqa: E501
      # noqa: E501
 
 
-    :rtype: Union[str, Tuple[str, int], Tuple[str, int, Dict[str, str]]
+    :rtype: str
     """
     return 'do some magic!'
 
@@ -24,6 +21,6 @@ def ready():  # noqa: E501
      # noqa: E501
 
 
-    :rtype: Union[str, Tuple[str, int], Tuple[str, int, Dict[str, str]]
+    :rtype: str
     """
     return 'do some magic!'