def upload_file(request):
if request.method == 'POST':
print(request.FILES)
all_files = request.FILES.getlist('files[]')
if len(all_files) > 0:
try:
uploaded_file = all_files[0]
file_name = uploaded_file.name
filename, file_extension = os.path.splitext(file_name)
if not file_extension in [".csv", ".h5", '.xlxs']:
return JsonResponse({
"status": "failure",
"message": "Unsupported file format"
})
# TODO: Check for file extension here
if not os.path.exists(settings.MEDIA_ROOT):
os.makedirs(settings.MEDIA_ROOT)
file_name = "{}_{}".format(time.time(), file_name)
file_path = os.path.join(settings.MEDIA_ROOT, file_name)
fout = open(file_path, 'wb+')
# Iterate through the chunks.
for chunk in uploaded_file.chunks():
fout.write(chunk)
fout.close()
# Save this file to database
dataset = Dataset(path=file_name)
dataset.save()
return JsonResponse({
'status': 'success',
'message': 'Data uploaded successfully',
'file_path': file_name,
"dataset_id": dataset.id
})
except Exception as e:
return JsonResponse({
'status':
'failure',
'message':
'Error:Upload failed:{}'.format(e)
})
else:
return JsonResponse({
"status": "failure",
"message": "No file found"
})
else:
print(request)
return JsonResponse({
'status': 'failure',
'message': 'Invalid request'
})
def make_dataset(user_id, file_id, filter_id):
"""
Function form DataSet from File with given id by applying given filter.
After filtration DataSet is added to DB
:param user_id: id of User which currently works with this data
:param file_id: id of a File from which should we get DataSet
:param filter_id: id of Filter which we apply to File and total amount of rows for DataSet
:return: id of created DataSet
"""
filters = Filter.query.get(
filter_id).params # getting params for filtering from DB
dataframe = dataframe_actualization(
file_id, user_id
) # getting actual DataFrame with dropped earlier DataSets formed from same File
result = filter_apply(
dataframe, filters
) # getting results from filtering function as a list of included rows indexes
result = [int(x) for x in result
] # transform numpy int[64] to regular int to store array in DB
new_dataframe = Dataset(file_id=file_id,
user_id=user_id,
included_rows=result,
filter_id=filter_id)
db.session.add(new_dataframe)
db.session.commit()
return new_dataframe.id
def test_one_article_no_compounds_dataset_model(self):
# Create article without compound
art = Article(pmid=12345,
journal='Test Journal',
year=2018,
volume='12',
issue='12',
pages='1-1000',
authors='Douglas Adams',
doi='10.1234/HHGTTG',
title='HHGTTG',
abstract='Test Abstract',
num_compounds=0)
# Get curator
curator = Curator.query.filter_by(username='******').first()
self.assertEqual(curator.username, 'test_user')
# Create empty dataset and add
ds = Dataset(curator=curator, articles=[art])
db.session.add(ds)
db.session.commit()
# Tests
self.assertEqual(Dataset.query.count(), 1)
self.assertEqual(Dataset.query.first().curator.username, 'test_user')
self.assertEqual(len(Dataset.query.first().articles), 1)
self.assertEqual(Dataset.query.first().articles[0].pmid, 12345)
def add_dataset():
tmp_dir = os.path.join(current_app.instance_path,
current_app.config["TEMP_DIR"])
dataset_dir = os.path.join(current_app.instance_path,
current_app.config["DATASET_DIR"])
form = AdminAddDatasetForm()
if form.validate_on_submit():
temp_filename = os.path.join(tmp_dir,
secure_filename(form.file_.data.filename))
if not os.path.exists(temp_filename):
flash("Internal error: temporary dataset disappeared.", "error")
return redirect(url_for("admin.add_dataset"))
name = get_name_from_dataset(temp_filename)
target_filename = os.path.join(dataset_dir, name + ".json")
if os.path.exists(target_filename):
flash("Internal error: file already exists!", "error")
return redirect(url_for("admin.add_dataset"))
os.rename(temp_filename, target_filename)
if not os.path.exists(target_filename):
flash("Internal error: file moving failed", "error")
return redirect(url_for("admin.add_dataset"))
is_demo = dataset_is_demo(target_filename)
dataset = Dataset(name=name,
md5sum=md5sum(target_filename),
is_demo=is_demo)
db.session.add(dataset)
db.session.commit()
flash("Dataset %r added successfully." % name, "success")
return redirect(url_for("admin.add_dataset"))
return render_template("admin/add.html", title="Add Dataset", form=form)
def insert_sample_datasets(self):
with open(self.datasets_file, 'r') as dataset_file:
reader = csv.reader(dataset_file)
next(reader)
for row in reader:
dataset = Dataset(dataset_id=row[0],
annex_uuid=row[1],
description=row[2],
owner_id=row[3],
download_path=row[4],
raw_data_url=row[5],
name=row[6],
modality=row[7],
version=row[8],
format=row[9],
category=row[10],
image=self.read_image(row[11]),
date_created=datetime.now(),
date_updated=datetime.now(),
is_private=row[12] == 'True')
db.session.add(dataset)
db.session.commit()
dataset_file.close()
def test_one_article_one_compound_dataset_model(self):
# Create compound
cmpd = Compound(name='Methane',
smiles='C',
source_organism='Saccharomyces cerevisiae')
# Create article with compound
art = Article(pmid=12345,
journal='Test Journal',
year=2018,
volume='12',
issue='12',
pages='1-1000',
authors='Douglas Adams',
doi='10.1234/HHGTTG',
title='HHGTTG',
abstract='Test Abstract',
num_compounds=1,
compounds=[cmpd])
# Get curator
curator = Curator.query.filter_by(username='******').first()
self.assertEqual(curator.username, 'test_user')
# Create empty dataset and add
ds = Dataset(curator=curator, articles=[art])
db.session.add(ds)
db.session.commit()
# Tests
self.assertEqual(Dataset.query.count(), 1)
self.assertEqual(len(Dataset.query.first().articles), 1)
self.assertEqual(Dataset.query.first().articles[0].pmid, 12345)
self.assertEqual(len(Dataset.query.first().articles[0].compounds), 1)
self.assertEqual(Dataset.query.first().articles[0].compounds[0].name,
'Methane')
def create_dataset():
name = request.form['name']
area = request.form['area']
source = request.form['source']
file_type = request.form['file_type']
link = request.form['link']
date_obtained = request.form['date_obtained']
tags = request.form['tags']
file = request.files['file']
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
filepath = os.path.join(datasets.config['UPLOAD_FOLDER'], filename)
if os.path.exists(filepath):
new_filename = '{}_{}.{}'.format(
filename.rsplit('.', 1)[0], datetime.now.strftime('%H%M'),
filename.rsplit('.', 1)[1])
new_filepath = os.path.join(datasets.config['UPLOAD_FOLDER'],
new_filename)
file.save(
os.path.join(datasets.config['UPLOAD_FOLDER'], new_filename))
new_dataset = Dataset(name=name,
area=area,
source=source,
file_type=file_type,
link=link,
date_obtained=date_obtained,
tags=tags,
file=new_filepath)
else:
file.save(os.path.join(datasets.config['UPLOAD_FOLDER'], filename))
new_dataset = Dataset(name=name,
area=area,
source=source,
file_type=file_type,
link=link,
date_obtained=date_obtained,
tags=tags,
file=filepath)
db.session.add(new_dataset)
db.session.commit()
return jsonify({'status': 'success'}), 200
def upload_file(self, file):
"""
Accepts FileStorage object
Saves original uploaded file and serialized DataFrame for this file.
Creates records in database
:param file: FileStorage
:return: IDs of created data set and file
"""
# Get check sum of file
hashed_file_name = f'{self.get_file_checksum(file)}'
# Change file name and save it under this name
file_extension = self.get_file_extension(file.filename)
file_full_name = f'{hashed_file_name}.{file_extension}'
file_path = os.path.join(self.files_dir, file_full_name)
# Send existing file instead of uploading a new one
if file_full_name in self.files:
_file = File.query.filter(File.path == file_full_name).first()
_dataset = Dataset.query.filter(
Dataset.file_id == _file.id).first()
logger.info(
'User {0} uploaded which already existed under id {1}'.format(
self.user_id, _file.id))
return 'Uploaded', _file.id, _dataset.id
file.seek(0)
file.save(file_path)
# Serialize uploaded file as DataFrame (Update when DataFrame interface is ready)
shape = self.serialize(file_full_name)
# Get attributes of file
file_attributes = self.get_attributes(file_path)
file_attributes['name'] = file.filename
file_attributes['rows'] = shape[0]
file_attributes['cols'] = shape[1]
# Save to db, update when dbm is ready
new_file = File(path=file_full_name, attributes=file_attributes)
db.session.add(new_file)
db.session.flush()
new_dataset = Dataset(user_id=self.user_id, file_id=new_file.id)
db.session.add(new_dataset)
db.session.commit()
logger.info('User {0} uploaded a new file {1}'.format(
self.user_id, new_file.id))
response = {
'file': {
'id': new_file.id,
'name': new_file.attributes['name'],
'size': new_file.attributes['size'],
'rows': new_file.attributes['rows']
},
'dataset_id': new_dataset.id
}
return response
def register_face():
form = RegistrationForm()
if form.validate_on_submit():
if form.images.data:
print(
"##############################################################\n"
)
print(form.images.data)
images = []
# random_hex = secrets.token_hex(8)
name = form.name.data
person = Person(name=name)
db.session.add(person)
db.session.commit()
id = Person.query.filter_by(name=name).first().id
has_at_least_one_image_with_single_face = False
for image in form.images.data:
# TODO see if there is one only one face in the image (because suppose if there are
# 2 persons in the image and the 2nd one tries to recognize himself then if id folder
# of 1st one comes first than the 2nd one's id folder, 2nd one will be recognized as
# 1st person as the photo is in 1st person's id folder)
face_image = faces.hasSingleFace(image)
if face_image is not None:
has_at_least_one_image_with_single_face = True
image_fn, image_path = save_image_to_dataset(
dir_name=str(id),
form_image_name=image.filename,
to_be_saved_image=face_image)
dataset = Dataset(image_file=image_fn, author=person)
db.session.add(dataset)
print(image_path)
images.append(image_fn)
if has_at_least_one_image_with_single_face is True:
db.session.commit()
faces.make_new_face_encodings()
flash(
f'Congratulations! Successfully registered the face as {form.name.data}. Try recognizing {form.name.data}.',
'success')
return redirect(
url_for('recognize_faces', title='Recognize Faces'))
else:
flash(
f'{form.name.data} not registered as there was no face in the image. Try providing different images.',
'danger')
return render_template('register_face.html',
title="Register Face",
selectedListElement="registerFace",
form=form)
return render_template('register_face.html',
title="Register Face",
selectedListElement="registerFace",
form=form)
def _seed_test_datasets_db(app):
"""
Seeds a set of test datasets populated from a static csv file
"""
from app import db
from app.models import User, Dataset, DatasetStats
dataset_csvfile = os.path.join(app.root_path, "../test/datasets.csv")
with open(dataset_csvfile, 'r') as data_csv:
csv_reader = csv.DictReader(data_csv)
for row in csv_reader:
dataset = Dataset(
dataset_id=row['dataset_id'],
annex_uuid=row['annex_uuid'],
description=row['description'],
owner_id=row['owner_id'],
download_path=row['download_path'],
raw_data_url=row['raw_data_url'],
name=row['name'],
modality=row['modality'],
version=row['version'],
format=row['format'],
category=row['category'],
date_created=datetime.utcnow(),
date_updated=datetime.utcnow(),
is_private=row['is_private'] == 'True'
)
db.session.add(dataset)
dataset_stats_csvfile = os.path.join(
app.root_path, "../test/datasets_stats.csv")
with open(dataset_stats_csvfile, 'r') as datastat_csv:
csv_reader = csv.DictReader(datastat_csv)
for row in csv_reader:
dataset_stat = DatasetStats(
dataset_id=row['dataset_id'],
size=row['size'],
files=row['files'],
sources=row['sources'],
num_subjects=row['num_subjects'],
num_downloads=row['num_downloads'],
num_likes=row['num_likes'],
num_views=row['num_views'],
date_updated=datetime.utcnow()
)
db.session.add(dataset_stat)
db.session.commit()
def new_dataset():
"""
Creates a new mock dataset to test
"""
dataset = Dataset(dataset_id="8de99b0e-5f94-11e9-9e05-52545e9add8e",
description="Human Brain phantom scans, Multiple MRI"
" scans of a single human phantom over 11"
" years, T1 weighted images and others on"
" 13 scanner in 6 sites accross North America."
" The data are available in minc format",
name="Multicenter Single Subject Human MRI Phantom",
version="1.0",
is_private=False,
fspath='./test/test_dataset')
return dataset
def test_empty_dataset_model(self):
"""
Create dataset for test_user with no data
"""
# Get curator
curator = Curator.query.filter_by(username='******').first()
self.assertEqual(curator.username, 'test_user')
# Create empty dataset and add
ds = Dataset(curator=curator)
db.session.add(ds)
db.session.commit()
# Tests
self.assertEqual(Dataset.query.count(), 1)
self.assertEqual(Dataset.query.first().curator_id, 2)
self.assertEqual(len(Dataset.query.first().articles), 0)
def seed_test_db():
from app import db
from app.models import User, Dataset, DatasetStats
# create an admin user (Not useful now, but at least we will have a user)
# import the current dataset information (to be replaced by dyanmic process)
dataset_csvfile = os.path.join(app.root_path, "../test/datasets.csv")
with open(dataset_csvfile, 'r') as data_csv:
csv_reader = csv.DictReader(data_csv)
for row in csv_reader:
dataset = Dataset(dataset_id=row['dataset_id'],
annex_uuid=row['annex_uuid'],
description=row['description'],
owner_id=row['owner_id'],
download_path=row['download_path'],
raw_data_url=row['raw_data_url'],
name=row['name'],
modality=row['modality'],
version=row['version'],
format=row['format'],
category=row['category'],
date_created=datetime.utcnow(),
date_updated=datetime.utcnow(),
is_private=row['is_private'] == 'True')
db.session.add(dataset)
dataset_stats_csvfile = os.path.join(app.root_path,
"../test/datasets_stats.csv")
with open(dataset_stats_csvfile, 'r') as datastat_csv:
csv_reader = csv.DictReader(datastat_csv)
for row in csv_reader:
dataset_stat = DatasetStats(
dataset_id=row['dataset_id'],
size=row['size'],
files=row['files'],
sources=row['sources'],
num_subjects=row['num_subjects'],
num_downloads=row['num_downloads'],
num_likes=row['num_likes'],
num_views=row['num_views'],
date_updated=datetime.utcnow())
db.session.add(dataset_stat)
db.session.commit()
def dataset():
form = DatasetForm()
form.datasets_choices()
if request.method == 'POST' and form.validate_on_submit():
logger.info(f'dataset: {form.dataset.data}, split: {form.split.data}, '
f'kfolds: {form.kfolds.data}')
# parameters used when the dataset was created.
details = form.dataset.data.split('_')
dataset = Dataset(file=form.dataset.data,
window=details[1].split('w')[-1],
aggregation=details[2].split('t')[-1],
size=details[3].split('.csv')[0].split('s')[-1],
split=form.split.data,
kfolds=form.kfolds.data)
db.session.add(dataset)
db.session.commit()
return redirect(url_for('setting.classifier'))
return render_template('setting/dataset.html', form=form)
def search_dataset():
qstring = request.args.get('query')
results, total = Dataset.search(qstring)
output = {}
output["total"] = total
output["results"] = []
for result in results:
values = {
'name': result.name,
'area': result.area,
'source': result.source,
'file_type': result.file_type,
'link': result.link,
'date_obtained': result.date_obtained,
'tags': result.tags,
'id': result.id,
}
output["results"].append(values)
return jsonify(output), 200
def insert_sample_datasets(self):
with open(self.datasets_file, 'r') as dataset_file:
reader = csv.reader(dataset_file)
next(reader)
for row in reader:
dataset = Dataset(id=row[0],
dataset_id=row[1],
owner_id=row[2],
name=row[3],
modality=row[4],
version=row[5],
format=row[6],
category=row[7],
date_created=datetime.now(),
date_updated=datetime.now(),
is_private=row[8] == 'True')
db.session.add(dataset)
db.session.commit()
dataset_file.close()
def new_dataset():
"""
Creastes a new mock dataset to test
"""
dataset = Dataset(dataset_id="8de99b0e-5f94-11e9-9e05-52545e9add8e",
annex_uuid="4fd032a1-220a-404e-95ac-ccaa3f7efcb7",
description="Human Brain phantom scans, Multiple MRI"
" scans of a single human phantom over 11"
" years, T1 weighted images and others on"
" 13 scanner in 6 sites accross North America."
" The data are available in minc format",
owner_id=1,
download_path="multicenter-phantom",
raw_data_url="https://phantom-dev.loris.ca",
name="Multicenter Single Subject Human MRI Phantom",
modality="Imaging",
version="1.0",
format="minc",
category="Phantom",
is_private=False)
return dataset
def push_docker_img(self, dir_name,current_user_id, name, report):
client = docker.from_env()
current_user_obj = User.query.get(current_user_id)
image_name = current_user_obj.username + '-' + name
repo_name = os.environ.get('DOCKER_REPO') + '/'
print(client.images.push(repository=repo_name + image_name), file=sys.stderr)
########## UPDATING DB ######################################################################
# add dataset to database
new_dataset = Dataset(url="https://hub.docker.com/raas/" + repo_name + image_name + "/",
author=current_user_obj,
name=name,
report=report)
db.session.add(new_dataset)
db.session.commit()
########## CLEANING UP ######################################################################
self.clean_up_datasets(dir_name)
print("Returning")
def new_dataset():
if request.method == 'POST':
print(request.form)
#if request.form['dataset_uploaded']:
# flash(f'Your dataset has been created!', 'success')
# return redirect(url_for('datasets.new_dataset'))
dataset = Dataset(title=request.form['title'], abstract=request.form['abstract'], category=request.form['category'])
db.session.add(dataset)
db.session.commit()
return json.dumps({"dataset_id": dataset.id})
form = DatasetForm()
if form.validate_on_submit():
print(f'datasets data: {form.datasets}')
# for files in form.datasets.getlist():
# print(filles)
return render_template('create_dataset.html', title='New Dataset',form=form, legend='New Dataset')
def run_command():
atlas.dbInit("mysql+pymysql", "jvansan", "", "127.0.0.1",
"np_atlas_2018_07")
sess = atlas.startSession()
curator = Curator.query.filter_by(username="******").first()
articles = get_first_N_article_with_compounds(sess, 100)
ds_articles = []
for art_compound in articles:
a = art_compound[0]
compounds = []
for c in art_compound[1]:
org = get_compound_origin(c, sess)
org_string = org.genus.name + " " + org.species
compounds.append(
Compound(name=c.names[0].name,
smiles=c.smiles,
source_organism=org_string))
# Make sure to sort the names of the compounds before insertion
compounds.sort(key=lambda x: x.name)
art = Article(pmid=a.pmid,
journal=a.journal.title,
year=a.year,
volume=a.volume,
issue=a.issue,
pages=a.pages,
authors=a.authors,
doi=a.doi,
title=a.title,
abstract=a.abstract,
num_compounds=len(compounds),
compounds=compounds)
ds_articles.append(art)
ds = Dataset(curator=curator, articles=ds_articles)
db.session.add(ds)
db.session.commit()
def _update_datasets(app):
"""
Updates from conp-datasets
"""
from app import db
from app.models import ArkId
from app.models import Dataset as DBDataset
from app.models import DatasetAncestry as DBDatasetAncestry
from sqlalchemy import exc
from datalad import api
from datalad.api import Dataset as DataladDataset
import fnmatch
import json
from pathlib import Path
import git
datasetsdir = Path(app.config['DATA_PATH']) / 'conp-dataset'
datasetsdir.mkdir(parents=True, exist_ok=True)
# Initialize the git repository object
try:
repo = git.Repo(datasetsdir)
except git.exc.InvalidGitRepositoryError:
repo = git.Repo.clone_from('https://github.com/CONP-PCNO/conp-dataset',
datasetsdir,
branch='master')
# Update to latest commit
origin = repo.remotes.origin
origin.pull('master')
repo.submodule_update(recursive=False, keep_going=True)
d = DataladDataset(path=datasetsdir)
if not d.is_installed():
api.clone(source='https://github.com/CONP-PCNO/conp-dataset',
path=datasetsdir)
d = DataladDataset(path=datasetsdir)
try:
d.install(path='', recursive=True)
except Exception as e:
print("\033[91m")
print("[ERROR ] An exception occurred in datalad update.")
print(e.args)
print("\033[0m")
return
print('[INFO ] conp-dataset update complete')
print('[INFO ] Updating subdatasets')
for ds in d.subdatasets():
print('[INFO ] Updating ' + ds['gitmodule_url'])
subdataset = DataladDataset(path=ds['path'])
if not subdataset.is_installed():
try:
api.clone(source=ds['gitmodule_url'], path=ds['path'])
subdataset = DataladDataset(path=ds['path'])
subdataset.install(path='')
except Exception as e:
print("\033[91m")
print(
"[ERROR ] An exception occurred in datalad install for " +
str(ds) + ".")
print(e.args)
print("\033[0m")
continue
# The following relates to the DATS.json files
# of the projects directory in the conp-dataset repo.
# Skip directories that aren't projects.
patterns = [app.config['DATA_PATH'] + '/conp-dataset/projects/*']
if not any(
fnmatch.fnmatch(ds['path'], pattern) for pattern in patterns):
continue
dirs = os.listdir(ds['path'])
descriptor = ''
for file in dirs:
if fnmatch.fnmatch(file.lower(), 'dats.json'):
descriptor = file
if descriptor == '':
print("\033[91m")
print('[ERROR ] DATS.json file can`t be found in ' + ds['path'] +
".")
print("\033[0m")
continue
try:
with open(os.path.join(ds['path'], descriptor), 'r') as f:
dats = json.load(f)
except Exception as e:
print("\033[91m")
print("[ERROR ] Descriptor file can't be read.")
print(e.args)
print("\033[0m")
continue
# use dats.json data to fill the datasets table
# avoid duplication / REPLACE instead of insert
dataset = DBDataset.query.filter_by(
dataset_id=ds['gitmodule_name']).first()
# pull the timestamp of the first commit in the git log for the dataset create date
createDate = datetime.utcnow()
try:
createTimeStamp = os.popen(
"git -C {} log --pretty=format:%ct --reverse | head -1".format(
ds['path'])).read()
createDate = datetime.fromtimestamp(int(createTimeStamp))
except Exception:
print("[ERROR ] Create Date couldnt be read.")
firstMergeDate = datetime.utcnow()
try:
firstMergeTimeStamp = os.popen(
"git -C {} log --pretty=format:%ct --reverse {} | head -1".
format(app.config['DATA_PATH'] + "/conp-dataset",
ds['path'])).read()
firstMergeDate = datetime.fromtimestamp(int(firstMergeTimeStamp))
except Exception:
print(
"[ERROR ] First merge date of the submodule dataset could not be read."
)
# last commit in the git log for the dataset update date
updateDate = datetime.utcnow()
try:
createTimeStamp = os.popen(
"git -C {} log --pretty=format:%ct | head -1".format(
ds['path'])).read()
updateDate = datetime.fromtimestamp(int(createTimeStamp))
except Exception:
print("[ERROR ] Update Date couldnt be read.")
# get the remote URL
remoteUrl = None
try:
remoteUrl = os.popen(
"git -C {} config --get remote.origin.url".format(
ds['path'])).read()
except Exception:
print("[ERROR ] Remote URL couldnt be read.")
if dataset is None:
dataset = DBDataset()
dataset.dataset_id = ds['gitmodule_name']
dataset.date_created = createDate
dataset.date_added_to_portal = firstMergeDate
if dataset.date_created != createDate:
dataset.date_created = createDate
# check for dataset ancestry
extraprops = dats.get('extraProperties', [])
for prop in extraprops:
if prop.get('category') == 'parent_dataset_id':
for x in prop.get('values', []):
if x.get('value', None) is None:
continue
datasetAncestry = DBDatasetAncestry()
datasetAncestry.id = str(uuid.uuid4())
datasetAncestry.parent_dataset_id = 'projects/' + \
x.get('value', None)
datasetAncestry.child_dataset_id = dataset.dataset_id
try:
db.session.merge(datasetAncestry)
db.session.commit()
except exc.IntegrityError:
# we already have a record of this ancestry
db.session.rollback()
if not dataset.date_added_to_portal:
dataset.date_added_to_portal = firstMergeDate
dataset.date_updated = updateDate
dataset.fspath = ds['path']
dataset.remoteUrl = remoteUrl
dataset.description = dats.get('description',
'No description in DATS.json')
dataset.name = dats.get('title', os.path.basename(dataset.dataset_id))
db.session.merge(dataset)
db.session.commit()
# if the dataset does not have an ARK identifier yet, generate it
dataset_with_ark_id_list = [
row[0] for row in db.session.query(ArkId.dataset_id).all()
]
if dataset.dataset_id not in dataset_with_ark_id_list:
new_ark_id = ark_id_minter(app, 'dataset')
save_ark_id_in_database(app, 'dataset', new_ark_id,
dataset.dataset_id)
print('[INFO ] ' + ds['gitmodule_name'] + ' updated.')
def update_face(person_id):
form = UpdateDatasetForm()
person = Person.query.get_or_404(person_id)
datasets = Dataset.query.filter_by(author=person).all()
print(
'###############################################################################'
)
print(person)
print(datasets)
print(
'###############################################################################'
)
if form.validate_on_submit():
if form.images.data:
print(
"##############################################################\n"
)
print(form.images.data)
images = []
# random_hex = secrets.token_hex(8)
has_at_least_one_image_with_single_face = False
for image in form.images.data:
# TODO see if there is one only one face in the image (because suppose if there are
# 2 persons in the image and the 2nd one tries to recognize himself then if id folder
# of 1st one comes first than the 2nd one's id folder, 2nd one will be recognized as
# 1st person as the photo is in 1st person's id folder)
# see if there is any image or not
if image.mimetype.find("image") == -1:
break
face_image = faces.hasSingleFace(image)
if face_image is not None:
has_at_least_one_image_with_single_face = True
image_fn, image_path = save_image_to_dataset(
dir_name=str(person_id),
form_image_name=image.filename,
to_be_saved_image=face_image)
dataset = Dataset(image_file=image_fn, author=person)
db.session.add(dataset)
print(image_path)
images.append(image_fn)
name = form.name.data
if name != person.name:
person.name = name
image_deleted_from_dataset = False
if form.images_to_be_deleted.data:
for image_id in form.images_to_be_deleted.data.split(";"):
dataset = Dataset.query.get(image_id)
path_to_image = './app/static/images/dataset/' + str(
person_id) + '/' + dataset.image_file
if os.path.exists(path_to_image):
image_deleted_from_dataset = True
os.remove(path_to_image)
db.session.delete(dataset)
db.session.commit()
# update dataset_faces.dat if either an image was deleted from dataset or new image was added
if has_at_least_one_image_with_single_face is True or image_deleted_from_dataset is True:
faces.make_new_face_encodings()
flash(f'Successfully updated {form.name.data}.', 'success')
return redirect(url_for('face', person_id=person_id))
else:
flash(f'{form.name.data} not updated.', 'danger')
return render_template('update_face.html',
title=person.name,
file_select=True,
enableDeletePersonPhoto=True,
datasets=datasets,
form=form)
elif request.method == 'GET':
form.name.data = person.name
return render_template('update_face.html',
title=person.name,
file_select=True,
enableDeletePersonPhoto=True,
datasets=datasets,
form=form)
def _update_datasets(app):
"""
Updates from conp-datasets
"""
from app import db, config
from app.models import Dataset as DBDataset
from datalad import api
from datalad.api import Dataset as DataladDataset
import fnmatch
import json
datasetspath = app.config['DATA_PATH']
d = DataladDataset(path=datasetspath + '/conp-dataset')
if not d.is_installed():
api.clone(source='https://github.com/CONP-PCNO/conp-dataset',
path=datasetspath + '/conp-dataset')
d = DataladDataset(path=datasetspath + '/conp-dataset')
d.install(path='', recursive=True)
try:
d.update(path='', merge=True, recursive=True)
except Exception as e:
print("\033[91m")
print("[ERROR ] An exception occurred in datalad update.")
print(e.args)
print("\033[0m")
return
print('[INFO ] conp-dataset update complete')
print('[INFO ] Updating subdatasets')
for ds in d.subdatasets():
print('[INFO ] Updating ' + ds['gitmodule_url'])
subdataset = DataladDataset(path=ds['path'])
if not subdataset.is_installed():
try:
api.clone(source=ds['gitmodule_url'], path=ds['path'])
subdataset = DataladDataset(path=ds['path'])
subdataset.install(path='')
except Exception as e:
print("\033[91m")
print(
"[ERROR ] An exception occurred in datalad install for " +
str(ds) + ".")
print(e.args)
print("\033[0m")
continue
dirs = os.listdir(ds['path'])
descriptor = ''
for file in dirs:
if fnmatch.fnmatch(file.lower(), 'dats.json'):
descriptor = file
if descriptor == '':
print("\033[91m")
print('[ERROR ] DATS.json file can`t be found in ' + ds['path'] +
".")
print("\033[0m")
continue
try:
with open(os.path.join(ds['path'], descriptor), 'r') as f:
dats = json.load(f)
except Exception as e:
print("\033[91m")
print("[ERROR ] Descriptor file can't be read.")
print(e.args)
print("\033[0m")
continue
# use dats.json data to fill the datasets table
# avoid duplication / REPLACE instead of insert
dataset = DBDataset.query.filter_by(
dataset_id=ds['gitmodule_name']).first()
if dataset is None:
dataset = DBDataset()
dataset.dataset_id = ds['gitmodule_name']
dataset.date_created = datetime.utcnow()
dataset.date_updated = datetime.utcnow()
dataset.fspath = ds['path']
dataset.description = dats.get('description',
'No description in DATS.json')
dataset.name = dats.get('title', os.path.basename(dataset.dataset_id))
db.session.merge(dataset)
db.session.commit()
print('[INFO ] ' + ds['gitmodule_name'] + ' updated.')
def _update_datasets(app):
"""
Updates from conp-datasets
"""
from app import db, config
from app.models import Dataset as DBDataset
from datalad import api
from datalad.api import Dataset as DataladDataset
import fnmatch
import json
from pathlib import Path
import git
datasetsdir = Path(app.config['DATA_PATH']) / 'conp-dataset'
datasetsdir.mkdir(parents=True, exist_ok=True)
# Initialize the git repository object
try:
repo = git.Repo(datasetsdir)
except git.exc.InvalidGitRepositoryError as e:
repo = git.Repo.clone_from(
'https://github.com/CONP-PCNO/conp-dataset',
datasetsdir,
branch='master'
)
# Update to latest commit
origin = repo.remotes.origin
origin.pull('master')
repo.submodule_update(recursive=False, keep_going=True)
d = DataladDataset(path=datasetsdir)
if not d.is_installed():
api.clone(
source='https://github.com/CONP-PCNO/conp-dataset',
path=datasetsdir
)
d = DataladDataset(path=datasetsdir)
try:
d.install(path='', recursive=True)
except Exception as e:
print("\033[91m")
print("[ERROR ] An exception occurred in datalad update.")
print(e.args)
print("\033[0m")
return
print('[INFO ] conp-dataset update complete')
print('[INFO ] Updating subdatasets')
for ds in d.subdatasets():
print('[INFO ] Updating ' + ds['gitmodule_url'])
subdataset = DataladDataset(path=ds['path'])
if not subdataset.is_installed():
try:
api.clone(
source=ds['gitmodule_url'],
path=ds['path']
)
subdataset = DataladDataset(path=ds['path'])
subdataset.install(path='')
except Exception as e:
print("\033[91m")
print("[ERROR ] An exception occurred in datalad install for " + str(ds) + ".")
print(e.args)
print("\033[0m")
continue
dirs = os.listdir(ds['path'])
descriptor = ''
for file in dirs:
if fnmatch.fnmatch(file.lower(), 'dats.json'):
descriptor = file
if descriptor == '':
print("\033[91m")
print('[ERROR ] DATS.json file can`t be found in ' + ds['path'] + ".")
print("\033[0m")
continue
try:
with open(os.path.join(ds['path'], descriptor), 'r') as f:
dats = json.load(f)
except Exception as e:
print("\033[91m")
print("[ERROR ] Descriptor file can't be read.")
print(e.args)
print("\033[0m")
continue
# use dats.json data to fill the datasets table
# avoid duplication / REPLACE instead of insert
dataset = DBDataset.query.filter_by(dataset_id=ds['gitmodule_name']).first()
if dataset is None:
dataset = DBDataset()
dataset.dataset_id = ds['gitmodule_name']
dataset.date_created = datetime.utcnow()
dataset.date_updated = datetime.utcnow()
dataset.fspath = ds['path']
dataset.description = dats.get('description', 'No description in DATS.json')
dataset.name = dats.get(
'title',
os.path.basename(dataset.dataset_id)
)
db.session.merge(dataset)
db.session.commit()
print('[INFO ] ' + ds['gitmodule_name'] + ' updated.')
from flask import abort, jsonify
from . import main
from app.models import Dataset
import json
import pydap.client
dataset = Dataset.objects(name='vic_conus_3km').first()
dataset.data = pydap.client.open_url(dataset.url)
@main.route("/")
def hello():
return "Hello World"
@main.route("/<api_key>/<location>", methods=['GET'])
def opendap_json(api_key=None, location=None):
try:
loc = location.split(',')
except:
abort(404)
try:
lat = float(loc[0])
lon = float(loc[1])
except:
abort(404)
if lat and lon:
location = json.loads(dataset.get_xy(lat=lat,lon=lon))
else:
return "error: provide latitude and longitude"
def create(request):
if request.method == 'POST':
dataset = Dataset()
dataset.owner = request.user
dataset.name = request.POST['name']
dataset.number_of_labels = request.POST['number_of_labels']
dataset.description = request.POST['description']
if not dataset.privacy_validation(request.POST['privacy']):
return render(request, '400.html', status=400)
dataset_file = request.FILES['dataset']
reader = csv.reader(dataset_file, encoding='utf-8')
header_list = reader.next()
label_name = request.POST.get('label_name', 'CLASS')
append_label_column = request.POST.get('append_label_column', False)
if not append_label_column:
label_index = header_list.index(label_name)
header_list.pop(label_index)
header_list.append(label_name)
dataset.header = csvlist_to_string(header_list).strip()
dataset.save()
samples_count = 0
for row_list in reader:
samples_count += 1
if not append_label_column:
label_string = row_list.pop(label_index)
row = csvlist_to_string(row_list).strip()
sample = Sample(dataset=dataset, data=row,
original_index=samples_count)
sample.save()
if not append_label_column and label_string:
label = Label(owner=request.user, sample=sample,
label=label_string)
label.save()
sample.times_labeled = 1
sample.save()
dataset.number_of_samples = samples_count
dataset.save()
return HttpResponseRedirect(
reverse('datasets_show', args=(dataset.id,)))
def load_dataset(directory=None):
"""Page to load new datasets from within HOST."""
data_dir = os.path.join(current_app.config['ABS_PATH'],
'static/datasets/preloaded')
# All raters
all_raters = request.args.get('all_raters', 0, type=int)
# Choices of directories to load in form
dir_choices = [
d for d in os.listdir(data_dir)
if os.path.isdir(os.path.join(data_dir, d))
]
dir_choices.sort()
info = {'directory': directory, 'new_imgs': 0}
if directory is not None:
# Save useful info for jinja template
info['model'] = Dataset.query.filter_by(name=directory).first()
# Check access before loading files
if info['model']:
info['access'] = current_user.has_access(info['model'])
info['saved_imgs'] = info['model'].images.count()
else:
info['access'] = True
info['saved_imgs'] = 0
if info['access']:
# Count the files in the directory
all_files = []
for root, _, files in os.walk(os.path.join(data_dir, directory)):
all_files.extend([
os.path.join(root, f) for f in files
if not f.startswith('.')
])
info['new_imgs'] = len(all_files) - info['saved_imgs']
form = LoadDatasetForm()
form.dir_name.choices = dir_choices
# Form submission must be restricted by access in template
if form.validate_on_submit():
if info['model']:
new_dataset = False
else:
# If dataset is not a Dataset Model (does not exist), create it
info['model'] = Dataset(name=form.dir_name.data,
creator=current_user)
db.session.add(info['model'])
new_dataset = True
flash(f"{info['model'].name} was created as an OPEN dataset",
'info')
if len(all_files) > 10:
current_user.launch_task('load_data',
f"Loading {info['new_imgs']} new images "
f"to {info['model'].name} dataset...",
icon='load',
alert_color='primary',
files=all_files,
dataset_name=info['model'].name,
new_dataset=new_dataset,
ignore_existing=True)
db.session.commit()
else:
try:
# Function returns number of uploaded images
loaded_imgs = load_data(all_files,
dataset=info['model'],
host=True,
new_dataset=new_dataset)
except OrphanDatasetError:
# If orphaned dataset, delete it
# TODO this somehow throws an error; look into this
# db.session.delete(info['model'])
flash(
'No new files were successfully loaded '
'leaving the dataset empty', 'warning')
else:
if not new_dataset and loaded_imgs == 0:
flash('No new files were successfully loaded', 'warning')
else:
flash(f'{loaded_imgs} file(s) successfully loaded!',
'success')
finally:
# Commit changes in database
db.session.commit()
return redirect(url_for('main.dashboard', all_raters=all_raters))
# Form validation errors
for _, error in form.errors.items():
flash(error[0], 'danger')
return render_template('data/load_dataset.html',
form=form,
title="Load Dataset",
dictionary=info,
all_raters=all_raters)
def upload_dataset():
"""Page to upload new dataset of MRI."""
data_dir = os.path.join(current_app.config['ABS_PATH'],
'static/datasets/uploaded')
# All raters
all_raters = request.args.get('all_raters', 0, type=int)
form = UploadDatasetForm()
if form.validate_on_submit():
files = request.files.getlist(form.dataset.name)
savedir = os.path.join(data_dir, form.dataset_name.data)
# If savedir does not exist; create it
if not os.path.isdir(savedir):
os.makedirs(savedir)
# Form checks that dataset does not exist already
# so there is no need to check here; just create it
dataset = Dataset(name=form.dataset_name.data,
creator=current_user,
private=form.privacy.data)
dataset.grant_access(current_user)
db.session.add(dataset)
privacy = 'a PRIVATE' if dataset.private else 'an OPEN'
flash(f"{dataset.name} was created as {privacy} dataset", 'info')
if len(files) > 10:
# Redis can't handle FileStorage
# First upload all files
files_uploaded = upload_data(files, savedir)
current_user.launch_task('load_data',
f'Uploading {len(files)} new images '
f'to {dataset.name} dataset...',
icon='upload',
alert_color='primary',
files=files_uploaded,
dataset_name=dataset.name,
new_dataset=True)
db.session.commit()
else:
try:
# Function returns number of uploaded images
loaded_imgs = load_data(files, dataset, savedir=savedir)
except OrphanDatasetError:
# If orphaned dataset, delete it
db.session.delete(dataset)
else:
# If not, that means at least one image was uploaded
# flash success with number of uploads
flash(f'{loaded_imgs} file(s) successfully loaded!', 'success')
finally:
# Commit changes in database
db.session.commit()
return redirect(url_for('main.dashboard', all_raters=all_raters))
for _, error in form.errors.items():
flash(error[0], 'danger')
return render_template('data/upload_dataset.html',
form=form,
all_raters=all_raters,
title='Upload Dataset')
def upload_dataset():
user = User.query.filter_by(UserAccountId=current_user.get_id()).first()
form = DatasetForm()
if form.submit.data and form.validate_on_submit():
odesc = Dataset.query.order_by(Dataset.OfferingId.desc()).first()
if not odesc:
o_id = 1
else:
o_id = odesc.OfferingId + 1
o_type = int(request.form['offering_type'])
df_ext = form.dataset_upload.data.filename.rsplit('.', 1)[1]
df_name = secure_filename(
str(user.UserAccountId) + '-' + str(o_id) + '-df.' + df_ext)
df_path = os.path.join(app.root_path, 'dataset-files', df_name)
form.dataset_upload.data.save(
os.path.join(app.root_path, 'dataset-files', df_name))
if form.sample_upload.data:
sf_ext = form.sample_upload.data.filename.rsplit('.', 1)[1]
sf_name = secure_filename(
str(user.UserAccountId) + '-' + str(o_id) + '-sf.' + sf_ext)
sf_path = os.path.join(app.root_path, 'sample-files', sf_name)
form.sample_upload.data.save(
os.path.join(app.root_path, 'sample-files', sf_name))
else:
sf_name = None
sf_path = None
lf_ext = form.license_upload.data.filename.rsplit('.', 1)[1]
lf_name = secure_filename(
str(user.UserAccountId) + '-' + str(o_id) + '-lf.' + lf_ext)
lf_path = os.path.join(app.root_path, 'license-files', lf_name)
form.license_upload.data.save(
os.path.join(app.root_path, 'license-files', lf_name))
if o_type == 1:
uf = 0
elif o_type == 2:
uf = int(form.update_frequency.data)
dataset = Dataset(OfferingName=form.offering_name.data, OfferingType=o_type, Category=form.category.data, \
Description=form.description.data, Region=form.region.data, DateCreated=form.date_created.data, \
DateLastUpdated=form.last_updated.data, UpdateFrequency=uf, DataFileName=df_name, DataFilePath=df_path, \
SampleFileName=sf_name, SampleFilePath=sf_path, LicenseFileName=lf_name, LicenseFilePath=lf_path, \
Price=form.price.data, owner=user)
db.session.add(dataset)
db.session.commit()
# new_row = [form.offering_name.data, user.UserName, form.category.data, form.region.data, o_type, uf, form.description.data, form.price.data]
# train_file = os.path.join(app.root_path, 'train.csv')
# with open(train_file,'a') as fd:
# writer = csv.writer(fd, lineterminator='\n')
# writer.writerow(new_row)
return redirect(url_for('my_offerings'))
if form.calc.data and form.offering_name.data and form.description.data and form.region.data:
o_type = int(request.form['offering_type'])
if o_type == 1:
uf = 0
elif o_type == 2:
uf = int(form.update_frequency.data)
data = {
'name': [form.offering_name.data],
'seller': [user.UserName],
'category': [form.category.data],
'region': [form.region.data],
'offering_type': [o_type],
'update_frequency': [uf],
'description': [form.description.data],
'price': [0]
}
df = pd.DataFrame(data)
train_file = os.path.join(app.root_path, 'train.csv')
sug_price = calc_price(df, train_file)
form.suggested_price.data = 'Suggested Price: $' + str(
round(sug_price, 2))
elif form.calc.data:
form.suggested_price.data = ''
flash(
'Name, Region and Description are required for suggesting price!')
return render_template('dataset-upload.html',
title='Upload Data',
form=form)
def create(request):
if request.method == 'POST':
dataset = Dataset()
dataset.owner = request.user
dataset.name = request.POST['name']
dataset.number_of_labels = request.POST['number_of_labels']
dataset.description = request.POST['description']
if not dataset.privacy_validation(request.POST['privacy']):
return render(request, '400.html', status=400)
dataset_file = request.FILES['dataset']
reader = csv.reader(dataset_file, encoding='utf-8')
header_list = reader.next()
label_name = request.POST.get('label_name', 'CLASS')
append_label_column = request.POST.get('append_label_column', False)
if not append_label_column:
label_index = header_list.index(label_name)
header_list.pop(label_index)
header_list.append(label_name)
dataset.header = csvlist_to_string(header_list).strip()
dataset.save()
samples_count = 0
for row_list in reader:
samples_count += 1
if not append_label_column:
label_string = row_list.pop(label_index)
row = csvlist_to_string(row_list).strip()
sample = Sample(dataset=dataset,
data=row,
original_index=samples_count)
sample.save()
if not append_label_column and label_string:
label = Label(owner=request.user,
sample=sample,
label=label_string)
label.save()
sample.times_labeled = 1
sample.save()
dataset.number_of_samples = samples_count
dataset.save()
return HttpResponseRedirect(
reverse('datasets_show', args=(dataset.id, )))