def delete_qib(qib_id):
try:
models.QIB.query.filter_by(id = qib_id).delete()
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_albums():
try:
all_albums = models.Album.query.all()
results = albums_schema.dump(all_albums)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_regions():
try:
all_regions = models.Region.query.all()
results = regions_schema.dump(all_regions)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_modalities():
try:
all_modalities = models.Modality.query.all()
results = modalities_schema.dump(all_modalities)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def upload_csv():
try:
file_name=''
album_name=''
qib_name=''
qib_description=''
csv_type=''
if request.form:
album_name = request.form['album_name']
qib_name = request.form['qib_name']
qib_description = request.form['qib_description']
file_name = request.form['file_name']
csv_type = request.form['csv_type']
if request.method == 'POST' and request.files:
data = pd.read_csv(request.files[file_name])
headers = data.columns.values.tolist()
csv_check = check_headers(headers, csv_type)
if csv_check == False:
return jsonify('Invalid columns')
else:
if csv_type == 'Custom QIB':
load_custom_filter_csv_to_db(data,album_name, qib_name,qib_description)
if csv_type == 'New QIB':
load_file_to_db(data,album_name,qib_name,qib_description)
if csv_type == 'Outcome list':
add_outcome(data)
return jsonify('OK')
except Exception:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_patients():
try:
all_patients = models.Patient.query.all()
results = patients_schema.dump(all_patients)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_features(qib_id):
try:
all_features_of_qib = db.session.query(models.QIBFeature.id_feature).filter(models.QIBFeature.id_qib == qib_id).subquery()
features = db.session.query(models.Feature).filter(models.Feature.id.in_(all_features_of_qib))
results = features_schema.dump(features)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_family(family_name):
try:
if request.json:
content = request.json
family = models.Family.query.filter_by(name = family_name).first()
family.name = content['name']
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def new_album():
try:
if request.json:
content = request.json
album = models.Album(content['name'],content['description'])
db.session.add(album)
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_qib(qib_id):
try:
if request.json:
content = request.json
qib = models.QIB.query.filter_by(id = qib_id).first()
qib.name = content['name']
qib.description = content['description']
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_studies_by_album(album_id):
try:
studies = []
study_albums = models.StudyAlbum.query.filter_by(id_album = album_id).all()
for study_album in study_albums:
study = models.Study.query.filter_by(id = study_album.id_study).first()
studies.append(study)
results = studies_schema.dump(studies)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def delete_family(family_name):
try:
family = models.Family.query.filter_by(name = family_name).first()
features = models.Feature.query.filter_by(id_family = family.id).all()
if len(features) > 0:
return jsonify("This feature family still has features. Cannot delete.")
db.session.delete(family)
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_album(album_id):
try:
if request.json:
content = request.json
album = models.Album.query.filter_by(id = album_id).first()
album.name = content['name']
album.description = content['description']
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_region(region_id):
try:
if request.json:
content = request.json
region = models.Region.query.filter_by(id = region_id).first()
region.name = content['name']
region.description = content['description']
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_modality(modality_id):
try:
if request.json:
content = request.json
modality = models.Modality.query.filter_by(id = modality_id).first()
modality.name = content['name']
modality.description = content['description']
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_feature(feature_id):
try:
if request.json:
content = request.json
feature = models.Feature.query.filter_by(id = feature_id).first()
feature.name = content['name']
family = models.Family.query.filter_by(name = content['family']).first()
feature.family = family
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def delete_album(album_id):
try:
qibs = models.QIB.query.filter_by(id_album = album_id).all()
print(qibs)
if len(qibs) > 0:
return jsonify("Album has children QIBs. Cannot delete.")
album = models.Album.query.filter_by(id = album_id).first()
db.session.delete(album)
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def tag_column(qib_id):
try:
if request.json:
content = request.json
print( content['outcome_column'])
qib = models.QIB.query.filter_by(id = qib_id).first()
qib.outcome_column = content['outcome_column']
qib.metadata_columns = content['metadata_columns']
db.session.commit()
results = qib_schema.dump(qib)
return jsonify(results)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def new_family():
try:
if request.json:
content = request.json
print(content)
family = models.Family.query.filter_by(name = content['name']).first()
if family is not None:
return jsonify("Family already exists.")
family = models.Family(name = content['name'])
db.session.add(family)
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_statistics():
try:
series = db.session.query(models.Series.id).count()
studies = db.session.query(models.Study.id).count()
patients = db.session.query(models.Patient.id).count()
qibs = db.session.query(models.QIB.id).count()
stat_dict = {}
stat_dict['series'] = series
stat_dict['studies'] = studies
stat_dict['patients'] = patients
stat_dict['qibs'] = qibs
return jsonify(stat_dict)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def edit_patient(patient_id):
try:
if request.json:
content = request.json
patient = models.Patient.query.filter_by(id = patient_id).first()
patient.first_name = content['first_name']
patient.last_name = content['last_name']
patient.birthdate = datetime.strptime(content['birthdate'], '%Y-%m-%d')
patient.gender = content['gender']
outcome = models.Outcome.query.filter_by(id_patient = patient_id).first()
outcome.plc_status = content['plc_status']
db.session.commit()
return jsonify("OK")
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_qib_features_by_qib(qib_id):
try:
all_qib_features = models.QIBFeature.query.filter_by(id_qib=qib_id).all()
df = convert_to_df(all_qib_features)
return df.to_json(orient='records')
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_families_features():
try:
all_families = models.Family.query.all()
all_features = models.Feature.query.all()
family_feature_dict = {}
for family in all_families:
family_feature_dict[family.name] = []
for feature in all_features:
if feature.family.name in family_feature_dict:
family_feature_dict[feature.family.name].append(feature_schema.dump(feature))
family_feature_list = []
for key, value in family_feature_dict.items():
result_dict={}
result_dict["family"] = key
result_dict["features"] = value
family_feature_list.append(result_dict)
return jsonify(family_feature_list)
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def generate_scatterplot_data(qib_id, feature_1, feature_2):
try:
feature_1 = models.Feature.query.filter_by(id = feature_1).scalar()
feature_2 = models.Feature.query.filter_by(id = feature_2).scalar()
all_qib_features = models.QIBFeature.query.filter(models.QIBFeature.id_qib == qib_id)\
.filter((models.QIBFeature.feature == feature_1) | (models.QIBFeature.feature == feature_2)).all()
df = convert_to_scatter_coords(all_qib_features,feature_1,feature_2)
return df.to_json(orient='values')
except Exception as err:
return jsonify(f"{err.__class__.__name__}: {err}")
def get_qibs():
try:
album = request.args.get('album', default = 0, type = int)
region = request.args.get('region', default = 0, type = int)
date = request.args.get('date', default = '*', type = str)
print(datetime.now())
if(album!=0 and region==0 and date=='*'):
all_qibs = models.QIB.query.filter_by(id_album=album).all()
elif(album==0 and region!=0 and date=='*'):
all_qibs = models.QIB.query.join(models.QIBFeature, models.QIB.id == models.QIBFeature.id_qib)\
.join(models.SeriesRegion, models.QIBFeature.id_series_region == models.SeriesRegion.id)\
.join(models.Region, models.Region.id == models.SeriesRegion.id_region)\
.filter(models.Region.id == region).all()
elif(album==0 and region==0 and date!='*'):
all_qibs = models.QIB.query.filter(models.QIB.time_stamp >= datetime.strptime(date, '%Y-%m-%d %H:%M:%S.%f')).all()
else:
all_qibs = models.QIB.query.all()
results = qibs_schema.dump(all_qibs)
return jsonify(results)
except Exception as err:
print(err)
return jsonify(f"{err.__class__.__name__}: {err}")
def greet():
return jsonify('Hello. This is the API for the feature manager.')
