Merge pull request #725 from neuroscout/report_warnings

Generate warnings in report

neuroscout/frontend/src/analysis_builder/Report.tsx

@@ -1,5 +1,5 @@
 import * as React from 'react';
-import { Button, Tabs, Collapse, Card, Tooltip, Icon, Select, Spin, Popconfirm } from 'antd';
+import { Alert, Button, Tabs, Collapse, Card, Tooltip, Icon, Select, Spin, Popconfirm } from 'antd';
 import vegaEmbed from 'vega-embed';
 
 import { OptionProps } from 'antd/lib/select';
@@ -33,6 +33,28 @@ class VegaPlot extends React.Component<{spec: string}, {}> {
   }
 }
 
+class Warnings extends React.Component<{warnings: string[]}> {
+  render() {
+    let alerts: any[] = [];
+    this.props.warnings.map((x, i) => {
+      alerts.push(
+        <Alert
+          message="Warning"
+          description={x}
+          type="warning"
+          showIcon={true}
+        />
+      );
+    });
+    return(
+      <div>
+      <br/>
+      {alerts}
+      </div>
+    );
+  }
+}
+
 class Plots extends React.Component<{matrices: string[], plots: any[], corr_plots: any[], runTitles: string[]}, {}> {
     plotContainer;
     constructor(props) {
@@ -68,12 +90,28 @@ class Plots extends React.Component<{matrices: string[], plots: any[], corr_plot
     }
 }
 
-class Tracebacks extends React.Component<{reportTraceback: string, compileTraceback: string}, {}> {
+export class Tracebacks extends React.Component<{traceback: string, message: string}, {}> {
     render() {
+      let display: any[] = [];
+      if (this.props.traceback) {
+        display.push(
+          <Alert
+            message={this.props.message}
+            description={
+              <div><p>{this.props.traceback}</p>
+              If you don't know what this error means, feel free to ask
+              on <a href="https://neurostars.org/">NeuroStars</a>.<br/>
+              If you believe this is a bug, please open an issue on open an
+              <a href="https://github.com/neuroscout/neuroscout/issues"> issue on GitHub</a>.
+              </div>}
+            type="error"
+            showIcon={true}
+          />
+        );
+      }
       return(
       <div>
-        <p>{this.props.reportTraceback}</p>
-        <p>{this.props.compileTraceback}</p>
+      {display}
       </div>
       );
     }
@@ -91,9 +129,9 @@ interface ReportState {
   matrices: string[];
   plots: string[];
   corr_plots: string[];
+  warnings: string[];
   reportTimestamp: string;
   reportTraceback: string;
-  compileTraceback: string;
   reportsLoaded: boolean;
   reportsPosted: boolean;
   compileLoaded: boolean;
@@ -111,12 +149,12 @@ export class Report extends React.Component<ReportProps, ReportState> {
       matrices: [],
       plots: [],
       corr_plots: [],
+      warnings: [],
       reportTimestamp: '',
       reportsLoaded: false,
       reportsPosted: false,
       compileLoaded: false,
       reportTraceback: '',
-      compileTraceback: '',
       selectedRunIds: ['' + this.props.runs[0].id],
       runTitles: [this.formatRun(this.props.runs[0])],
       warnVisible: false
@@ -164,6 +202,11 @@ export class Report extends React.Component<ReportProps, ReportState> {
     let state = {...this.state};
     jwtFetch(`${domainRoot}/api/analyses/${id}/report?run_id=${this.state.selectedRunIds}`)
     .then((res) => {
+      if (res.warnings) {
+        state.warnings = res.warnings;
+      } else {
+        state.warnings = [];
+      }
       if (res.status === 'OK') {
         if (res.result === undefined) {
           return;
@@ -187,7 +230,6 @@ export class Report extends React.Component<ReportProps, ReportState> {
       } else {
         return;
       }
-
       state.reportsLoaded = true;
       this.setState({...state});
     });
@@ -211,9 +253,6 @@ export class Report extends React.Component<ReportProps, ReportState> {
       .then((res) => {
         state.status = res.status;
         state.compileLoaded = true;
-        if (res.traceback) {
-          state.compileTraceback = res.traceback;
-        }
         this.setState({...state});
       });
     }
@@ -254,13 +293,13 @@ export class Report extends React.Component<ReportProps, ReportState> {
   }
 
   filterRuns = (inputValue: string, option:  React.ReactElement<OptionProps>): boolean => {
-    
+
     if (option.props.children) {
       return ('' + option.props.children).includes(inputValue);
     }
     return false;
   }
- 
+
   formatRun = (run: Run) => {
     let ret = '';
     if (!!run.subject) {
@@ -362,17 +401,20 @@ export class Report extends React.Component<ReportProps, ReportState> {
               corr_plots={this.state.corr_plots}
               runTitles={this.state.runTitles}
             />
+
+            {(this.state.warnings.length > 0) && <Warnings warnings={this.state.warnings} />}
+
+            {(this.state.reportTraceback) &&
+            <div>
+              <br/>
+              <Tracebacks
+                message="Report failed to generate"
+                traceback={this.state.reportTraceback}
+              />
+            <br/></div>}
           </Spin>
         </Card>
         <br/>
-        {(this.state.reportTraceback || this.state.compileTraceback) &&
-        <div>
-        <Card title="Errors" key="errors">
-          <Tracebacks
-            reportTraceback={this.state.reportTraceback}
-            compileTraceback={this.state.compileTraceback}
-          />
-        </Card><br/></div>}
       </div>
     );
   }

neuroscout/frontend/src/analysis_builder/Status.tsx

@@ -5,7 +5,7 @@ import { jwtFetch } from '../utils';
 import { Analysis } from '../coretypes';
 import { StatusTag } from '../HelperComponents';
 import { api } from '../api';
-
+import { Tracebacks } from './Report';
 const domainRoot = config.server_url;
 
 export class DLLink extends React.Component<{status?: string, analysisId?: string}, {}> {
@@ -163,8 +163,8 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
       }
       jwtFetch(`${domainRoot}/api/analyses/${id}/compile`)
       .then((res) => {
-        if (res.compile_traceback) {
-          this.setState({compileTraceback: res.compile_traceback});
+        if (res.traceback) {
+          this.setState({compileTraceback: res.traceback});
         }
       });
   }
@@ -273,20 +273,6 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
           <br/>
         </div>
       }
-      {(this.props.status === 'FAILED') &&
-        <div>
-          <h3>Analysis Failed to Compile</h3>
-          <p>
-            Oh no! It looks like your analysis failed to compile.
-            Once you make changes to fix the analysis you can re-run it below.
-            If the issue remains, please file a
-            <a href="https://github.com/neuroscout/neuroscout/issues"> bugreport</a>.
-          </p>
-          <Card title="Errors" key="errors">
-            <pre>{this.state.compileTraceback}</pre>
-          </Card>
-        </div>
-      }
       {(this.props.status === 'DRAFT' || this.props.status === 'FAILED') &&
         <Submit
           status={this.props.status}
@@ -295,6 +281,16 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
           private={this.props.private}
         />
       }
+      {(this.props.status === 'FAILED') &&
+        <div>
+          <br/>
+          <Tracebacks
+            message="Analysis failed to compile"
+            traceback={this.state.compileTraceback}
+          />
+          <br/>
+        </div>
+      }
       {(this.props.status === 'PENDING' || this.props.status === 'SUBMITTING') &&
         <div>
           <h3>Analysis Pending Generation</h3>

neuroscout/models/analysis.py

@@ -109,6 +109,7 @@ class Report(db.Model):
     generated_at = db.Column(db.DateTime, default=datetime.datetime.utcnow)
     task_id = db.Column(db.Text)   # Celery task id
     result = db.Column(JSONB)  # JSON result from Celery (once finished)
+    warnings = db.Column(JSONB, default=[])
     traceback = db.Column(db.Text)
 
     status = db.Column(db.Text, default='PENDING')

neuroscout/populate/modify.py

@@ -31,7 +31,7 @@ def delete_task(dataset, task):
     db.session.commit()
 
 
-def extend_extracted_objects(dataset_name, **selectors):
+def extend_extracted_objects(dataset_name, task_name, **selectors):
     """ Links RunStimuli for newly ingest runs in a Dataset,
         for all ExtractedFeatures. Also links derived Stimuli with new Runs.
         Args:
@@ -42,8 +42,8 @@ def extend_extracted_objects(dataset_name, **selectors):
     run_ids = Run.query
     for key, value in selectors.items():
         run_ids = run_ids.filter(getattr(Run, key).in_(value))
-    runs = run_ids.join(Dataset).filter_by(
-        name=dataset_name)
+    runs = run_ids.join(Task).filter_by(name=task_name).join(
+        Dataset).filter_by(name=dataset_name)
 
     # Create RunStimulus associations with derived stimuli
     new_rs = []
@@ -69,7 +69,7 @@ def extend_extracted_objects(dataset_name, **selectors):
         ExtractedEvent).join(Stimulus).join(
             RunStimulus).filter(RunStimulus.run_id.in_(run_ids)).all()
 
-    create_predictors(efs, dataset_name, run_ids)
+    create_predictors(efs, dataset_name, task_name, run_ids)
 
 
 def update_annotations(mode='predictors', **kwargs):

neuroscout/schemas/analysis.py

@@ -150,6 +150,8 @@ class ReportSchema(Schema):
     generated_at = fields.Time(description='Time report was generated')
     result = fields.Dict(description='Links to report resources')
     status = fields.Str(description='Report status')
+    warnings = fields.List(
+        fields.Str(), description='Report warnings')
     traceback = fields.Str(
         description='Traceback of generation error.')
 

neuroscout/tasks/report.py

@@ -6,7 +6,8 @@
 from .utils.build import build_analysis, impute_confounds
 from .utils.viz import plot_design_matrix, plot_corr_matrix, sort_dm
 from .utils.io import (
-    dump_analysis, update_record, PathBuilder, write_jsons, write_tarball)
+    update_record, PathBuilder, write_jsons, write_tarball, analysis_to_json)
+from .utils.warnings import pre_warnings
 
 MIN_CLI_VERSION = '0.3.3'
 
@@ -20,31 +21,27 @@ def compile(flask_app, hash_id, run_ids=None, build=False):
         build (bool): Validate in pybids?
     """
     FILE_DATA = Path(flask_app.config['FILE_DIR'])
+    analysis_object = Analysis.query.filter_by(hash_id=hash_id).one()
 
     try:
-        analysis_object = Analysis.query.filter_by(hash_id=hash_id).one()
-    except Exception as e:
-        return {
-            'traceback': f'Error loading {hash_id} from db /n {str(e)}'
-            }
-    try:
-        a_id, analysis, resources, pes, bids_dir = dump_analysis(
-            hash_id)
+        a_id, analysis, resources, pes, bids_dir = analysis_to_json(
+            hash_id, run_ids)
     except Exception as e:
         update_record(
             analysis_object,
             exception=e,
             traceback='Error deserializing analysis'
         )
         raise
+
     try:
         tmp_dir, bundle_paths, _ = build_analysis(
             analysis, pes, bids_dir, run_ids, build=build)
     except Exception as e:
         update_record(
             analysis_object,
             exception=e,
-            traceback='Error validating analysis'
+            traceback='Error building analysis'
         )
         raise
 
@@ -94,30 +91,32 @@ def generate_report(flask_app, hash_id, report_id,
     """
     FILE_DATA = Path(flask_app.config['FILE_DIR'])
     domain = flask_app.config['SERVER_NAME']
+    report_object = Report.query.filter_by(id=report_id).one()
 
     try:
-        report_object = Report.query.filter_by(id=report_id).one()
+        _, analysis, resources, pes, bids_dir = analysis_to_json(
+            hash_id, run_ids)
     except Exception as e:
-        return {
-            'traceback': f'Error loading {report_id} from db /n {str(e)}'
-            }
+        update_record(
+            report_object,
+            exception=e,
+            traceback='Error deserializing analysis'
+        )
+        raise
 
     try:
-        a_id, analysis, resources, pes, bids_dir = dump_analysis(
-            hash_id)
+        pre_warnings(analysis, pes, report_object)
     except Exception as e:
         update_record(
             report_object,
             exception=e,
-            traceback='Error deserializing analysis'
+            traceback='Error generating warnings'
         )
-        raise
 
     try:
         _, _, bids_analysis = build_analysis(
             analysis, pes, bids_dir, run_ids)
     except Exception as e:
-        # Todo: In future, could add more messages here
         update_record(
             report_object,
             exception=e,