Merge pull request #837 from neuroscout/oct_small_fixes

Various UI improvements + Pybids 0.12.3
neuroscout · Oct 26, 2020 · 4948699 · 4948699
2 parents a846313 + 7adfb03
commit 4948699
Show file tree

Hide file tree

Showing 28 changed files with 208 additions and 89 deletions.
diff --git a/celery_worker/requirements.txt b/celery_worker/requirements.txt
@@ -11,7 +11,7 @@ sklearn
 networkx==1.9
 celery
 hashids==1.2.0
-marshmallow==2.19.1
+marshmallow==3.7.1
 psycopg2==2.8.3
 redis
 pandas==0.23
@@ -22,6 +22,7 @@ duecredit==0.6.1
 SQLAlchemy==1.3.0
 Flask-Caching==1.3.3
 flask_jwt
+shortuuid==1.0.1
 sentry-sdk==0.13.0
-pybids==0.10.1
+pybids==0.12.3
 Werkzeug==0.15.3
diff --git a/neuroscout/Dockerfile b/neuroscout/Dockerfile
@@ -22,6 +22,7 @@ RUN npm install -g yarn
 COPY requirements.txt /usr/src/app/
 COPY optional_requirements.txt /usr/src/app
 RUN pip install setuptools==45
+RUN pip uninstall -y enum34
 RUN pip install --no-cache-dir -r requirements.txt
 RUN pip install --no-cache-dir -r optional_requirements.txt
 RUN python -m pliers.support.download

diff --git a/neuroscout/core.py b/neuroscout/core.py
@@ -62,7 +62,9 @@
         ('UserPredictorListResource', 'user/predictors'),
         ('UserPredictorCollectionResource', 'user/collections'),
         ('TaskResource', 'tasks/<int:task_id>'),
-        ('TaskListResource', 'tasks')
+        ('TaskPredictorsResource', 'tasks/<int:task_id>/predictors'),
+        ('TaskListResource', 'tasks'),
+        ('ImageVersionResource', 'image_version')
     ])
 
 

diff --git a/neuroscout/frontend/src/AnalysisList.tsx b/neuroscout/frontend/src/AnalysisList.tsx
@@ -44,7 +44,7 @@ export class AnalysisListTable extends React.Component<AnalysisListProps> {
         title: 'Name',
         render: (text, record: AppAnalysis) => (
           <Link to={`/builder/${record.id}`}>
-            <div className="recordName">{record.name}</div>
+            <div className="recordName">{record.name ? record.name : 'Untitled'}</div>
           </Link>
         ),
         sorter: (a, b) => a.name.localeCompare(b.name)

diff --git a/neuroscout/frontend/src/Home.tsx b/neuroscout/frontend/src/Home.tsx
@@ -2,16 +2,17 @@
  Home component for the homepage
 */
 import * as React from 'react';
-import { Divider, Row, Col, Button, Card, Alert } from 'antd';
+import { Divider, Row, Col, Button, Card } from 'antd';
 import { MainCol } from './HelperComponents';
+import { UserStore } from './user';
 
 const titleStyle: any = {
   textAlign: ('center' as React.CSSProperties),
   fontSize: '20px',
   padding: '0px 0px 0px 0px'
 };
 
-class Home extends React.Component<{}, {}> {
+class Home extends React.Component<UserStore, {}> {
   render() {
     return (
 
@@ -24,9 +25,19 @@ class Home extends React.Component<{}, {}> {
          <div className="splashText">A platform for fast and flexible re-analysis of (naturalistic) fMRI studies</div>
          <br/><br/>
          <div className="splashButtonParent">
-         <Button size="large" className="splashButton" type="primary" href="/public">
+         <Button size="large" className="splashButton" type="default" href="/public">
             Browse public analyses
-         </Button>
+         </Button> <br/>
+         {this.props.loggedIn === false &&
+           <Button
+                size="large"
+                className="splashButton"
+                type="primary"
+                onClick={e => this.props.update({ openSignup: true })}
+           >
+              Sign up to get started!
+           </Button>
+         }
          </div>
          </div>
          <br/>

diff --git a/neuroscout/frontend/src/Routes.tsx b/neuroscout/frontend/src/Routes.tsx
@@ -21,7 +21,7 @@ export default class Routes extends React.Component<AppState, {}> {
           exact={true}
           path="/"
           render={props =>
-            <Home />
+            <Home {...this.props.user} />
            }
         />
         <Route
@@ -123,7 +123,7 @@ export default class Routes extends React.Component<AppState, {}> {
       <Route
         path="/profile/:user_name"
         render={props => {
-          return (<PublicProfile 
+          return (<PublicProfile
             user_name={props.match.params.user_name}
             datasets={this.props.datasets}
             cloneAnalysis={this.props.cloneAnalysis}

diff --git a/neuroscout/frontend/src/analysis_builder/Builder.tsx b/neuroscout/frontend/src/analysis_builder/Builder.tsx
@@ -149,7 +149,11 @@ class EditDetails extends React.Component<editDetailsProps, editDetailsState> {
   }
 
   init(props: editDetailsProps) {
-    return {newName: props.name, newDescription: props.description, visible: []};
+    return {
+      newName: props.name,
+      newDescription: props.description,
+      visible: props.name ? [] : ['1']
+    };
   }
 
   update() {
@@ -162,11 +166,11 @@ class EditDetails extends React.Component<editDetailsProps, editDetailsState> {
 
   render() {
     return (
-      <div>
+      <div className="editDetails">
       <Collapse bordered={false} activeKey={this.state.visible} onChange={this.onChange}>
         <Panel header="Edit Analysis Details" key="1">
           <Form layout="vertical">
-            <FormItem label="Name" required={true}>
+            <FormItem label="Name">
               <Input
                 placeholder="Name your analysis"
                 value={this.state.newName}
@@ -410,11 +414,6 @@ export default class AnalysisBuilder extends React.Component<BuilderProps & Rout
       return new Promise(() => {return false; });
     }
 
-    if (!analysis.name) {
-      displayError(Error('Analysis cannot be saved without a name'));
-      return new Promise(() => {return false; });
-    }
-
     const apiAnalysis: ApiAnalysis = {
       name: analysis.name,
       description: analysis.description,
@@ -616,9 +615,6 @@ export default class AnalysisBuilder extends React.Component<BuilderProps & Rout
       update[nextTab + 'Active' ] = true;
       if (this.state.activeTab === 'overview') {
         // need name and runids
-        if (this.state.analysis.name.length < 1) {
-          // how
-        }
         if (this.state.analysis.runIds.length < 1) {
         }
       } else if (!this.preTabChange(nextTab as TabName)) {
@@ -1133,7 +1129,7 @@ export default class AnalysisBuilder extends React.Component<BuilderProps & Rout
                     updateSelectedTaskId={this.updateState('selectedTaskId')}
                   />
                   {this.navButtons(
-                    !(!!this.state.analysis.name && this.state.analysis.runIds.length > 0 && selectedTaskId !== null),
+                    !(this.state.analysis.runIds.length > 0 && selectedTaskId !== null),
                     false
                   )}
                   <br/>
@@ -1284,14 +1280,15 @@ export default class AnalysisBuilder extends React.Component<BuilderProps & Rout
                   <h2>Finalize and Run</h2>
                   <StatusTab
                     status={analysis.status}
+                    name={analysis.name}
                     analysisId={analysis.analysisId}
                     confirmSubmission={this.confirmSubmission}
                     private={analysis.private || false}
                     updateAnalysis={this.updateAnalysis}
                     userOwns={this.props.userOwns}
                     modified_at={analysis.modified_at}
                   >
-                  {this.props.userOwns && !isDraft &&
+                  {this.props.userOwns &&
                       <EditDetails
                         name={analysis.name}
                         description={analysis.description}

diff --git a/neuroscout/frontend/src/analysis_builder/Overview.tsx b/neuroscout/frontend/src/analysis_builder/Overview.tsx
@@ -262,7 +262,6 @@ export class OverviewTab extends React.Component<OverviewTabProps, OverviewTabSt
                   placeholder="You can change this later"
                   value={analysis.name}
                   onChange={this.updateAnalysisFromEvent('name')}
-                  required={true}
                   min={1}
                 />
               </Col>

diff --git a/neuroscout/frontend/src/analysis_builder/Review.tsx b/neuroscout/frontend/src/analysis_builder/Review.tsx
@@ -160,7 +160,7 @@ export class Review extends React.Component<ReviewProps, {}> {
 
     return (
       <Card
-        title={'Overview of ' + (Name ? Name : 'No Name')}
+        title={'Overview of ' + (Name ? Name : 'Untitled')}
       >
         Author: <Link to={`/profile/${this.props.user_name}`}> {this.props.user_name} </Link>
         <p>{Description ? Description : 'No description.'}</p>

diff --git a/neuroscout/frontend/src/analysis_builder/Status.tsx b/neuroscout/frontend/src/analysis_builder/Status.tsx
@@ -53,6 +53,7 @@ class PubAccess extends React.Component<PubAccessProps, {}> {
 type submitProps = {
   status?: string,
   analysisId?: string,
+  name?: string,
   modified_at?: string;
   confirmSubmission: (build: boolean) => void,
   private: boolean,
@@ -99,6 +100,12 @@ export class Submit extends React.Component<submitProps, {tosAgree: boolean, val
     let validateChange = this.validateChange.bind(this);
     return(
       <div>
+        {!this.props.name &&
+          <span>
+           <br/><Alert message="Analysis needs name to be generated" type="warning" showIcon={true} closable={true} />
+          </span>
+        }
+        <br/>
         <h3>Terms for analysis generation:</h3>
         <ul>
           <li>I agree that once I submit my analysis, I will not be able to delete or edit it.</li>
@@ -131,7 +138,7 @@ export class Submit extends React.Component<submitProps, {tosAgree: boolean, val
           hidden={!this.props.analysisId}
           onClick={this.props.confirmSubmission.bind(this, this.state.validate)}
           type={'primary'}
-          disabled={!this.state.tosAgree || !['DRAFT', 'FAILED'].includes(status)}
+          disabled={!this.state.tosAgree || !['DRAFT', 'FAILED'].includes(status) || !this.props.name}
         >
           Generate
         </Button>
@@ -142,15 +149,20 @@ export class Submit extends React.Component<submitProps, {tosAgree: boolean, val
 
 type statusTabState = {
   compileTraceback: string,
-  nvUploads?: any
+  nvUploads?: any,
+  imageVersion: string
 };
 
 export class StatusTab extends React.Component<submitProps, statusTabState> {
   constructor(props) {
     super(props);
     this.state = {
       compileTraceback: '',
+      imageVersion: ''
     };
+  }
+
+  componentDidMount() {
     if ((this.props.analysisId !== undefined)) {
       this.getTraceback(this.props.analysisId);
       api.getNVUploads(this.props.analysisId).then(nvUploads => {
@@ -159,6 +171,11 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
         }
      });
     }
+    api.getImageVersion().then((version) => {
+      if (!!version) {
+        this.setState({imageVersion: `:${version}`});
+      }
+    });
   }
 
   getTraceback(id) {
@@ -260,19 +277,20 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
         <DateTag modified_at={this.props.modified_at} />
         <StatusTag status={this.props.status} analysisId={this.props.analysisId} />
       </div>
+      {this.props.children}
       {(this.props.status === 'PASSED') &&
         <div>
           <h3>Analysis Passed</h3>
           <p>
             {this.props.userOwns && 'Congratulations, your analysis has been compiled!'}
             Run the analysis with this this command, replacing '/local/outputdirectory' with a local directory.
-            See the <a href="https://github.com/neuroscout/neuroscout-cli">neuroscout-cli documentation </a>
+            See the <a href="https://neuroscout.github.io/neuroscout/cli/">neuroscout-cli documentation </a>
              for more information.
           </p>
           <pre>
             <code>
               docker run --rm -it -v /local/outputdirectory:/out
-              neuroscout/neuroscout-cli run /out {this.props.analysisId}
+              {` neuroscout/neuroscout-cli${this.state.imageVersion}`} run /out {this.props.analysisId}
             </code>
           </pre>
           <Card size="small" title="System Requirements" style={{ width: 400 }}>
@@ -286,6 +304,7 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
       {(this.props.status === 'DRAFT' || this.props.status === 'FAILED') &&
         <Submit
           status={this.props.status}
+          name={this.props.name}
           analysisId={this.props.analysisId}
           confirmSubmission={this.props.confirmSubmission}
           private={this.props.private}
@@ -308,7 +327,6 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
         </div>
       }
       {this.state.nvUploads && this.nvStatus(this.state.nvUploads)}
-      {this.props.children}
       </div>
     );
   }

diff --git a/neuroscout/frontend/src/analysis_builder/transforms.ts b/neuroscout/frontend/src/analysis_builder/transforms.ts
@@ -13,7 +13,7 @@ const transformDefinitions: Transformation[] = [
     Name: 'Scale',
     Demean: true,
     Rescale: true,
-    ReplaceNA: 'None' as ReplaceNA
+    ReplaceNA: 'after' as ReplaceNA
   },
   {
     Name: 'Orthogonalize',

diff --git a/neuroscout/frontend/src/api.ts b/neuroscout/frontend/src/api.ts
@@ -236,5 +236,13 @@ export const api = {
   },
   getPublicProfile: (user_name: string): Promise<ApiUser & {statusCode: number}> => {
     return jwtFetch(`${domainRoot}/api/user/${user_name}`);
+  },
+  getImageVersion: (): Promise<string> => {
+    return jwtFetch(`${domainRoot}/api/image_version`).then((res) => {
+      if (res.version) {
+        return res.version;
+      }
+      return '';
+    });
   }
 };
diff --git a/neuroscout/frontend/src/css/App.css b/neuroscout/frontend/src/css/App.css
@@ -152,3 +152,8 @@ pre {
 .profileName {
     margin: 0 0 0 10px;
 }
+
+.editDetails .ant-collapse-borderless {
+    background-color: #fff;
+    border: 0px;
+}
diff --git a/neuroscout/models/analysis.py b/neuroscout/models/analysis.py
@@ -18,7 +18,7 @@ class Analysis(db.Model):
     id = db.Column(db.Integer, primary_key=True)
     hash_id = db.Column(db.Text, unique=True)
 
-    name = db.Column(db.Text, nullable=False)
+    name = db.Column(db.Text)
     description = db.Column(db.Text)
     predictions = db.Column(db.Text, default='')
     private = db.Column(db.Boolean, default=True)

diff --git a/neuroscout/requirements.txt b/neuroscout/requirements.txt
@@ -11,7 +11,7 @@ dataclasses==0.7
 decorator==4.0.11
 docopt==0.6.2
 duecredit==0.6.1
-pybids==0.10.1
+pybids==0.12.3
 pynv==0.2
 Flask==1.1.1
 flask-apispec==0.10.0
@@ -66,6 +66,7 @@ sentry-sdk[flask]==0.13
 soundfile
 pytesseract
 SQLAlchemy==1.3.0
+shortuuid==1.0.1
 tqdm==4.11.2
 webargs==6.1.1
 Werkzeug==0.15.3

diff --git a/neuroscout/resources/__init__.py b/neuroscout/resources/__init__.py
@@ -5,10 +5,11 @@
                        AnalysisBundleResource, AnalysisFullResource,
                        AnalysisResourcesResource, ReportResource,
                        AnalysisFillResource, AnalysisUploadResource,
-                       BibliographyResource)
+                       BibliographyResource, ImageVersionResource)
 from .dataset import DatasetResource, DatasetListResource
 from .predictor import (PredictorListResource, PredictorResource,
                         PredictorCollectionCreateResource,
+                        TaskPredictorsResource,
                         PredictorCollectionResource, prepare_upload,
                         PredictorEventListResource)
 from .run import RunResource, RunListResource
@@ -51,6 +52,8 @@
     'UserPredictorCollectionResource',
     'UserListResource',
     'TaskResource',
+    'TaskPredictorsResource',
     'TaskListResource',
+    'ImageVersionResource',
     'prepare_upload'
 ]
diff --git a/neuroscout/resources/analysis/__init__.py b/neuroscout/resources/analysis/__init__.py
@@ -3,7 +3,8 @@
 from .endpoints import (AnalysisResource, AnalysisRootResource,
                         AnalysisBundleResource, CloneAnalysisResource,
                         AnalysisFullResource, AnalysisResourcesResource,
-                        AnalysisFillResource, BibliographyResource)
+                        AnalysisFillResource, BibliographyResource,
+                        ImageVersionResource)
 from .reports import (CompileAnalysisResource, ReportResource,
                       AnalysisUploadResource)
 
@@ -18,5 +19,6 @@
     'BibliographyResource',
     'CloneAnalysisResource',
     'CompileAnalysisResource',
-    'ReportResource'
+    'ReportResource',
+    'ImageVersionResource'
     ]