-
Notifications
You must be signed in to change notification settings - Fork 12
/
root.py
259 lines (237 loc) · 12.1 KB
/
root.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
# @author: Gunnar Schaefer
# Reno Bowen
import os
import json
import datetime
import tempfile
import subprocess
from tg import config, expose, flash, lurl, request, redirect, response
from tg.i18n import ugettext as _, lazy_ugettext as l_
import webob.exc
import nimsdata.medimg.nimsmontage
import nimsutil
from nimsgears.model import *
from nimsgears.lib.base import BaseController
from nimsgears.controllers.auth import AuthController
from nimsgears.controllers.pub import PubController
from nimsgears.controllers.error import ErrorController
from nimsgears.controllers.experiment import ExperimentController
from nimsgears.controllers.session import SessionController
from nimsgears.controllers.epoch import EpochController
from nimsgears.controllers.dataset import DatasetController
from nimsgears.controllers.user import UserController
__all__ = ['RootController']
store_path = config.get('store_path')
temp_path = config.get('temp_path')
class RootController(BaseController):
"""Root controller for the nimsgears application."""
auth = AuthController()
pub = PubController()
error = ErrorController()
experiment = ExperimentController()
session = SessionController()
epoch = EpochController()
dataset = DatasetController()
user = UserController()
@expose('nimsgears.templates.index')
def index(self):
"""Handle the front-page."""
return dict(page='index')
@expose('nimsgears.templates.about')
def about(self):
"""Handle the 'about' page."""
return dict(page='about')
@expose('nimsgears.templates.environ')
def environ(self):
"""This method showcases TG's access to the wsgi environment."""
return dict(environment=request.environ)
@expose('nimsgears.templates.login')
def login(self, came_from=lurl('/')):
"""Start the user login."""
login_counter = request.environ['repoze.who.logins']
if login_counter > 0:
flash(_('Wrong credentials.'), 'warning')
return dict(page='login', login_counter=str(login_counter), came_from=came_from)
@expose()
def post_login(self, came_from=lurl('/')):
"""
Redirect the user to the initially requested page on successful
authentication or redirect her back to the login page if login failed.
"""
if not request.identity:
login_counter = request.environ['repoze.who.logins'] + 1
redirect('/login', params=dict(came_from=came_from, __logins=login_counter))
redirect(came_from)
@expose()
def post_logout(self, came_from=lurl('/')):
"""Redirect the user to the home page on logout."""
redirect('/')
@expose('nimsgears.templates.pyramid', render_params={'doctype': None})
def pyramid(self, **kwargs):
user = request.identity['user'] if request.identity else User.get_by(uid=u'@public')
ds = Dataset.get(kwargs['dataset_id'])
if user.has_access_to(ds):
db_file = os.path.join(store_path, ds.relpath, ds.filenames[0])
return dict(zip(['dataset_id', 'tile_size', 'x_size', 'y_size'], (ds.id,) + nimsdata.medimg.nimsmontage.get_info(db_file)))
@expose('nimsgears.templates.qa_report', render_params={'doctype': None})
def qa_report(self, **kwargs):
user = request.identity['user'] if request.identity else User.get_by(uid=u'@public')
ds = Dataset.get(kwargs['dataset_id'])
if user.has_access_to(ds) and len(ds.filenames)>0:
json_file = [f for f in ds.filenames if f.endswith('.json')][0]
qa_file = os.path.join(store_path, ds.relpath, json_file)
with open(qa_file) as fp:
qa = json.load(fp)
if isinstance(qa, list):
# Old-style qa format
qa = qa[0]
version = 0.1
else:
version = qa['version']
return dict(dataset_id=ds.id, version=version, tsnr=round(qa['temporal SNR (median)'],2), num_spikes=len(qa['spikes']))
@expose(content_type='application/json')
def qa_data(self, *args):
user = request.identity['user'] if request.identity else User.get_by(uid=u'@public')
data_name,dataset_id = args[0].rsplit('.', 1)[0].split('_')
print((data_name,dataset_id))
ds = Dataset.get(int(dataset_id))
if user.has_access_to(ds) and len(ds.filenames)>0:
json_file = [f for f in ds.filenames if f.endswith('.json')][0]
qa_file = os.path.join(store_path, ds.relpath, json_file)
with open(qa_file) as fp:
qa = json.load(fp)
if isinstance(qa, list):
# Old-style qa format
qa = qa[0]
version = 0.1
else:
version = qa['version']
if data_name=='motion':
md = qa['mean displacement']
if version<1.0:
md[0] = md[1]
rel_md = [0] + [round(md[i]-md[i-1],3) for i in range(1,len(md))]
else:
rel_md = qa['relative displacement']
d = [{'key':"absolute",'color':"blue",'values':[{'x':t,'y':d} for t,d in zip(qa['frame #'],md)]},
{'key':"relative",'color':"cyan",'values':[{'x':t,'y':d} for t,d in zip(qa['frame #'],rel_md)]}]
json_str = json.dumps(d)
elif data_name=='tsz':
vals = []
color_scale = 239/(len(qa['timeseries zscore'])-1)
for sl,tsz in enumerate(qa['timeseries zscore']):
c = "#10" + hex(sl*color_scale+16)[2:] + hex(255-sl*color_scale)[2:]
vals.append({'key':"slice%d"%sl,'color':c,'values':[{'x':t,'y':d} for t,d in zip(qa['frame #'], tsz)]})
json_str = json.dumps(vals)
else:
json_str = ''
return json_str
@expose(content_type='image/jpeg')
def pyramid_tile(self, *args):
user = request.identity['user'] if request.identity else User.get_by(uid=u'@public')
dataset_id, z, x, y = map(int, args[0].rsplit('.', 1)[0].split('_'))
ds = Dataset.get(dataset_id)
if user.has_access_to(ds):
del response.pragma
response.etag = args[0]
response.cache_control = 'max-age = 86400'
response.last_modified = ds.updatetime
return nimsdata.medimg.nimsmontage.get_tile(os.path.join(store_path, ds.relpath, ds.filenames[0]), z, x, y)
@expose(content_type='application/octet-stream')
def file(self, **kwargs):
user = request.identity['user'] if request.identity else User.get_by(uid=u'@public')
if 'id' in kwargs and 'filename' in kwargs:
ds = Dataset.get(kwargs['id'])
filepath = os.path.join(store_path, ds.relpath, kwargs['filename'])
if user.has_access_to(ds, u'Read-Only' if (ds.kind == u'primary' or ds.kind == u'secondary') else u'Anon-Read'):
if os.path.exists(filepath):
response.content_disposition = 'attachment; filename=%s' % kwargs['filename'].encode('utf-8')
response.content_length = os.path.getsize(filepath) # not actually working
return open(filepath, 'r')
else:
raise webob.exc.HTTPNotFound()
else:
raise webob.exc.HTTPForbidden()
@expose(content_type='application/x-tar')
def download(self, **kwargs):
user = request.identity['user'] if request.identity else User.get_by(uid=u'@public')
db_results = []
epoch_paths = []
symlinks = []
temp_dir = tempfile.mkdtemp(dir=temp_path)
if 'id_dict' in kwargs and 'sess' in kwargs['id_dict']:
id_list = [int(id) for id in json.loads(kwargs['id_dict'])['sess']]
db_query = (DBSession.query(Session, Experiment, ResearchGroup, Dataset, Epoch)
.join(Subject, Session.subject)
.join(Experiment, Subject.experiment)
.join(ResearchGroup, Experiment.owner)
.join(Epoch, Session.epochs)
.join(Dataset, Epoch.datasets)
.filter(Session.id.in_(id_list)))
if kwargs.get('raw'):
db_results = db_query.filter(Dataset.kind != u'web').all()
else:
db_results = db_query.filter((Dataset.kind == u'peripheral') | (Dataset.kind == u'derived')).all()
elif 'id_dict' in kwargs and 'epoch' in kwargs['id_dict']:
id_list = [int(id) for id in json.loads(kwargs['id_dict'])['epoch']]
db_query = (DBSession.query(Session, Experiment, ResearchGroup, Dataset, Epoch)
.join(Subject, Session.subject)
.join(Experiment, Subject.experiment)
.join(ResearchGroup, Experiment.owner)
.join(Epoch, Session.epochs)
.join(Dataset, Epoch.datasets)
.filter(Epoch.id.in_(id_list)))
if kwargs.get('raw'):
db_results = db_query.filter(Dataset.kind != u'web').all()
else:
db_results = db_query.filter((Dataset.kind == u'peripheral') | (Dataset.kind == u'derived')).all()
elif 'id_dict' in kwargs and 'dataset' in kwargs['id_dict']:
id_list = [int(id) for id in json.loads(kwargs['id_dict'])['dataset']]
db_results = (DBSession.query(Dataset, Epoch, Session, Experiment, ResearchGroup)
.join(Epoch, Dataset.container)
.join(Session, Epoch.session)
.join(Subject, Session.subject)
.join(Experiment, Subject.experiment)
.join(ResearchGroup, Experiment.owner)
.filter(Dataset.id.in_(id_list))
.all())
for r in db_results:
if user.has_access_to(r.Dataset, u'Read-Only' if (r.Dataset.kind == u'primary' or r.Dataset.kind == u'secondary') else u'Anon-Read'):
if kwargs.get('legacy'):
ep = '%s/nims/%s/%s/%s' % (temp_dir, r.ResearchGroup.gid, r.Experiment.name, r.Session.legacy_dirname)
else:
ep = '%s/nims/%s/%s/%s/%s' % (temp_dir, r.ResearchGroup.gid, r.Experiment.name, r.Session.dirname, r.Epoch.dirname)
epoch_paths.append(ep)
for filename in r.Dataset.filenames:
if kwargs.get('legacy'):
name, sep, ext = filename.partition('.')
if name.endswith('_B0'): ext = '_B0.%s' % ext
elif name.endswith('_physio'): ext = '_physio.%s' % ext
elif name.endswith('_dicoms'): ext = '_dicoms.%s' % ext
else: ext = '.%s' % ext
sl_name = '%04d_%02d_%s%s' % (r.Epoch.series, r.Epoch.acq, r.Epoch.description, ext)
else:
sl_name = filename
cur_outfile = os.path.join(ep, sl_name)
while cur_outfile in [i[1] for i in symlinks]:
name, sep, ext = sl_name.partition('.')
sl_name = name + '+' + sep + ext
cur_outfile = os.path.join(ep, sl_name)
symlinks += [(os.path.join(store_path, r.Dataset.relpath, filename), cur_outfile)]
for ep in set(epoch_paths):
try:
os.makedirs(ep)
except OSError as err:
if err.errno!=17:
raise
for sl in symlinks:
try:
os.symlink(*sl)
except:
with open('/tmp/NIMS_last_download_err.txt', 'w') as f:
for s in symlinks:
f.write(str(s) + '\n')
raise
tar_proc = subprocess.Popen('tar -chf - -C %s nims; rm -r %s' % (temp_dir, temp_dir), shell=True, stdout=subprocess.PIPE)
response.content_disposition = 'attachment; filename=%s_%s' % ('nims', datetime.datetime.now().strftime('%Y%m%d_%H%M%S'))
return tar_proc.stdout