fix bug in updating studies

Author: m-murphy

src/sample-db-app/src/app/containers/app.ts

@@ -48,12 +48,12 @@ export class AppComponent {
   showSidenav$: Observable<boolean>;
 
   toolbarButtons = [
-    {
-      icon: 'arrow_back',
-      action: back(),
-      color: 'accent',
-      tooltip: 'Go Back'
-    }
+  //   {
+  //     icon: 'arrow_back',
+  //     action: back(),
+  //     color: 'accent',
+  //     tooltip: 'Go Back'
+  //   }
   ];
 
   constructor(private store: Store<fromRoot.State>) {

src/sample-db-app/src/app/effects/study.ts

@@ -13,7 +13,7 @@ import { empty } from 'rxjs/observable/empty';
 import { of } from 'rxjs/observable/of';
 import { go, replace, search, show, back, forward } from '@ngrx/router-store';
 
-import { Study } from '../models/study';
+import { Study, StudyEntry } from '../models/study';
 import { StudyService } from '../services/study';
 import * as study from '../actions/study';
 
@@ -73,8 +73,8 @@ export class StudyEffects {
     .map(toPayload)
     .switchMap(payload => {
       return this.studyService.updateStudy(payload)
-        .mergeMap((updatedStudy: Study) => {
-          return [ new study.LoadOneAction({study: updatedStudy}), go('study') ]
+        .mergeMap((updatedStudyEntry: StudyEntry) => {
+          return [ new study.LoadOneAction(updatedStudyEntry), go('study') ];
         })
         .catch(err => {
           if (err.status < 500 && err.status > 400) {

src/sample-db-app/src/app/services/study.ts

@@ -60,20 +60,28 @@ export class StudyService {
       });
   }
 
-  createStudy(study: Study): Observable<Study> {
+  createStudy(study: Study): Observable<StudyEntry> {
     return this.http.post(`${this.API_PATH}/study`, {'study': study}, {headers: this.headers})
       .map(res => res.json())
       .map(res => {
-        if (Object.keys(res.error).length === 0) {
+        if (Object.keys(res.error.study).length === 0 &&
+            Object.keys(res.error.specimen).length === 0 &&
+            Object.keys(res.error.study_subject).length === 0) {
           return res.data;
         } else {
           throw(new Error(JSON.stringify(res.error)));
         }
       })
-      .map((study: Study) => {
-        study.created = new Date(study.created);
-        study.last_updated = new Date(study.last_updated);
-        return study;
+      .map((studyEntry: StudyEntry) => {
+        studyEntry.study.created = new Date(studyEntry.study.created);
+        studyEntry.study.last_updated = new Date(studyEntry.study.last_updated);
+        studyEntry.specimen = studyEntry.specimen.map(specimen => {
+          if (specimen.collection_date) {
+            specimen.collection_date = new Date(specimen.collection_date);
+          }
+          return specimen;
+        });
+        return studyEntry;
       });
   }
 
@@ -89,7 +97,7 @@ export class StudyService {
       });
   }
 
-  updateStudy(study: Study): Observable<Study> {
+  updateStudy(study: Study): Observable<StudyEntry> {
     return this.createStudy(study);
   }
 

src/sample-db-py/sample_db/app.py

@@ -72,7 +72,7 @@ def create_study(self, title, short_code, is_longitudinal, lead_person, descript
         return study
 
     def get_study(self, study_id):
-        # type: (int) -> Tuple[Study, List[StudySubject], List[Specimen]]
+        # type: (int) -> Tuple[Study, List[StudySubject], List[Specimen], List[MatrixTube]]
         """
         Get a study
         :param study_id: study ID
@@ -91,28 +91,36 @@ def _get_study_by_short_code(session, short_code):
         return study
 
     def edit_study(self, study):
-        # type: (Study) -> Study
+        # type: (Study) -> Tuple[Study, List[StudySubject], List[Specimen], List[MatrixTube]]
         with self._session_scope() as session:
             old_study = session.query(Study).get(study.id)
             old_study.title = study.title
             old_study.description = study.description
             old_study.short_code = study.short_code
             old_study.is_longitudinal = study.is_longitudinal
             old_study.lead_person = study.lead_person
-        return old_study
+            study_subjects = session.query(StudySubject).filter(StudySubject.study_id == old_study.id).all() # type: list[StudySubject]
+            specimens = session.query(Specimen).join(StudySubject).filter(StudySubject.study_id == old_study.id).all() # type: list[Specimen]
+            matrix_tubes = session.query(MatrixTube).join(Specimen).join(StudySubject).filter(StudySubject.study_id == old_study.id).all()
+        return old_study, study_subjects, specimens, matrix_tubes
 
     def update_study(self, id, d):
-        # type: (int, dict) -> Study
+        # type: (int, dict) -> Tuple[Study, List[StudySubject], List[Specimen], List[MatrixTube]]
         with self._session_scope() as session:
             with session.no_autoflush:
                 study = session.query(Study).get(id)
                 study.update(d)
-        return study
+            study_subjects = session.query(StudySubject).filter(
+                StudySubject.study_id == study.id).all()  # type: list[StudySubject]
+            specimens = session.query(Specimen).join(StudySubject).filter(
+                StudySubject.study_id == study.id).all()  # type: list[Specimen]
+            matrix_tubes = session.query(MatrixTube).join(Specimen).join(StudySubject).filter(
+                StudySubject.study_id == study.id).all()
+        return study, study_subjects, specimens, matrix_tubes
 
     def delete_study(self, study):
         # type: (Study) -> boolean
         with self._session_scope() as session:
-            print study
             s = session.query(Study).get(study.id)
             session.delete(s)
         return True

src/sample-db-py/sample_db/views.py

@@ -107,16 +107,35 @@ def create_or_update_study():
             if not study.get('id'):
                 try:
                     study = db.create_study(**study)
+                    study_subjects = []
+                    specimens = []
+                    matrix_tubes = []
                 except IntegrityError as e:
                     raise InvalidUsage(parse_integrity_error(e), status_code=403)
             else:
                 try:
                     study_id = study.pop('id')
-                    study = db.update_study(study_id, study)
+                    study, study_subjects, specimens, matrix_tubes = db.update_study(study_id, study)
                 except IntegrityError as e:
                     raise InvalidUsage(parse_integrity_error(e), status_code=403)
-            d, err = study_schema.dump(study)
-            res = jsonify(sucess=True, data=d, error=err)
+            study_entries, study_error = study_schema.dump(study)
+            study_subject_entries, study_subject_error = study_subject_schema.dump(study_subjects, many=True)
+            specimen_entries, specimen_error = specimen_schema.dump(specimens, many=True)
+            matrix_tube_entries, matrix_tube_error = matrix_tube_schema.dump(matrix_tubes, many=True)
+            print study_subject_entries, specimen_entries, matrix_tube_entries
+            d = {
+                'study': study_entries,
+                'study_subject': study_subject_entries,
+                'specimen': specimen_entries,
+                'matrix_tube': matrix_tube_entries
+            }
+            err = {
+                'study': study_error,
+                'study_subject': study_subject_error,
+                'specimen': specimen_error,
+                'matrix_tube': matrix_tube_error
+            }
+            res = jsonify(data=d, error=err)
             return res
         except IntegrityError as e:
             raise InvalidUsage(parse_integrity_error(e), status_code=403)