# @author: Gunnar Schaefer, Kevin S. Hahn
import logging
log = logging.getLogger('nimsapi')
import os
import re
import copy
import shutil
import difflib
import hashlib
import tarfile
import datetime
import markdown
import nimsdata
import base
import tempdir as tempfile
def hrsize(size):
if size < 1000:
return '%d%s' % (size, 'B')
for suffix in 'KMGTPEZY':
size /= 1024.
if size < 10.:
return '%.1f%s' % (size, suffix)
if size < 1000.:
return '%.0f%s' % (size, suffix)
return '%.0f%s' % (size, 'Y')
def sort_file(db, filepath, digest, store_path):
filename = os.path.basename(filepath)
try:
log.info('Parsing %s' % filename)
dataset = nimsdata.parse(filepath)
except nimsdata.NIMSDataError:
return 415, 'Can\'t parse %s' % filename
else:
log.info('Sorting %s' % filename)
# TODO: bail, if any required params are not set
acquisition_spec, acquisition_id = update_db(db, dataset)
acquisition_path = os.path.join(store_path, acquisition_id[-3:] + '/' + acquisition_id)
if not os.path.exists(acquisition_path):
os.makedirs(acquisition_path)
file_spec = copy.deepcopy(acquisition_spec)
file_spec['files'] = {'$elemMatch': {'type': dataset.nims_file_type, 'state': dataset.nims_file_state, 'kinds': dataset.nims_file_kinds}}
file_info = dict(
name=dataset.nims_file_name,
ext=dataset.nims_file_ext,
size=os.path.getsize(filepath),
sha1=digest,
#hash=dataset.nims_hash, TODO: datasets should be able to hash themselves (but not here)
type=dataset.nims_file_type,
kinds=dataset.nims_file_kinds,
state=dataset.nims_file_state,
)
success = db.acquisitions.update(file_spec, {'$set': {'files.$': file_info}})
if not success['updatedExisting']:
db.acquisitions.update(acquisition_spec, {'$push': {'files': file_info}})
shutil.move(filepath, acquisition_path + '/' + dataset.nims_file_name + dataset.nims_file_ext)
log.debug('Done %s' % filename)
return 200, 'Success'
def update_db(db, dataset):
existing_group_ids = [g['_id'] for g in db.groups.find(None, ['_id'])]
group_id_matches = difflib.get_close_matches(dataset.nims_group_id, existing_group_ids, cutoff=0.8)
if len(group_id_matches) == 1:
group_id = group_id_matches[0]
project_name = dataset.nims_project or 'untitled'
else:
group_id = 'unknown'
project_name = dataset.nims_group_id + ('/' + dataset.nims_project if dataset.nims_project else '')
group = db.groups.find_one({'_id': group_id})
project_spec = {'gid': group['_id'], 'name': project_name}
project = db.projects.find_and_modify(
project_spec,
{'$setOnInsert': dict(group=group.get('name'), permissions=group['roles'], files=[])},
upsert=True,
new=True,
)
# project timestamp and timezone are inherited from latest acquisition
if dataset.nims_metadata_status and project.get('timestamp', dataset.nims_timestamp - datetime.timedelta(1)) < dataset.nims_timestamp:
db.projects.update(project_spec, {'$set': dict(timestamp=dataset.nims_timestamp, timezone=dataset.nims_timezone)})
session_spec = {'uid': dataset.nims_session_id}
session = db.sessions.find_and_modify(
session_spec,
{
'$setOnInsert': dict(project=project['_id'], permissions=project['permissions'], files=[]),
'$set': entity_metadata(dataset, dataset.session_properties, session_spec), # session_spec ensures non-empty $set
'$addToSet': {'domains': dataset.nims_file_domain},
},
upsert=True,
new=True,
)
# session timestamp and timezone are inherited from earliest acquisition
if dataset.nims_metadata_status and session.get('timestamp', dataset.nims_timestamp + datetime.timedelta(1)) > dataset.nims_timestamp:
db.sessions.update(session_spec, {'$set': dict(timestamp=dataset.nims_timestamp, timezone=dataset.nims_timezone)})
acquisition_spec = {'uid': dataset.nims_acquisition_id}
acquisition = db.acquisitions.find_and_modify(
acquisition_spec,
{
'$setOnInsert': dict(session=session['_id'], permissions=session['permissions'], files=[]),
'$set': entity_metadata(dataset, dataset.acquisition_properties, acquisition_spec), # acquisition_spec ensures non-empty $set
'$addToSet': {'types': {'$each': [{'domain': dataset.nims_file_domain, 'kind': kind} for kind in dataset.nims_file_kinds]}},
},
upsert=True,
new=True,
)
return acquisition_spec, str(acquisition['_id'])
def entity_metadata(dataset, properties, metadata={}, parent_key=''):
metadata = copy.deepcopy(metadata)
if dataset.nims_metadata_status is not None:
parent_key = parent_key and parent_key + '.'
for key, attributes in properties.iteritems():
if attributes['type'] == 'object':
metadata.update(entity_metadata(dataset, attributes['properties'], parent_key=key))
else:
value = getattr(dataset, attributes['field']) if 'field' in attributes else None
if value or value == 0: # drop Nones and empty iterables
metadata[parent_key + key] = value
return metadata
class Core(base.RequestHandler):
"""/nimsapi """
def head(self):
"""Return 200 OK."""
self.response.set_status(200)
def get(self):
"""Return API documentation"""
resources = """
Resource | Description
:--------------------------------------------------------|:-----------------------
nimsapi/login | user login
[(nimsapi/sites)] | local and remote sites
[(nimsapi/roles)] | user roles
nimsapi/upload | upload
nimsapi/download | download
[(nimsapi/log)] | log messages
[(nimsapi/search)] | search
[(nimsapi/users)] | list of users
[(nimsapi/users/count)] | count of users
[(nimsapi/users/schema)] | schema for single user
nimsapi/users/*<uid>* | details for user *<uid>*
[(nimsapi/groups)] | list of groups
[(nimsapi/groups/count)] | count of groups
[(nimsapi/groups/schema)] | schema for single group
nimsapi/groups/*<gid>* | details for group *<gid>*
[(nimsapi/projects)] | list of projects
[(nimsapi/projects/count)] | count of projects
[(nimsapi/projects/schema)] | schema for single project
nimsapi/projects/*<pid>* | details for project *<pid>*
nimsapi/projects/*<pid>*/sessions | list sessions for project *<pid>*
[(nimsapi/sessions/count)] | count of sessions
[(nimsapi/sessions/schema)] | schema for single session
nimsapi/sessions/*<sid>* | details for session *<sid>*
nimsapi/sessions/*<sid>*/move | move session *<sid>* to a different project
nimsapi/sessions/*<sid>*/acquisitions | list acquisitions for session *<sid>*
[(nimsapi/acquisitions/count)] | count of acquisitions
[(nimsapi/acquisitions/schema)] | schema for single acquisition
nimsapi/acquisitions/*<aid>* | details for acquisition *<aid>*
[(nimsapi/collections)] | list of collections
[(nimsapi/collections/count)] | count of collections
[(nimsapi/collections/schema)] | schema for single collection
nimsapi/collections/*<cid>* | details for collection *<cid>*
nimsapi/collections/*<cid>*/sessions | list of sessions for collection *<cid>*
nimsapi/collections/*<cid>*/acquisitions?session=*<sid>* | list of acquisitions for collection *<cid>*, optionally restricted to session *<sid>*
"""
if self.debug:
resources = re.sub(r'\[\((.*)\)\]', r'[\1](\1?user=%s)' % self.uid, resources)
else:
resources = re.sub(r'\[\((.*)\)\]', r'[\1](\1)', resources)
resources = resources.replace('<', '<').replace('>', '>').strip()
self.response.headers['Content-Type'] = 'text/html; charset=utf-8'
self.response.write('<html>\n')
self.response.write('<head>\n')
self.response.write('<title>NIMSAPI</title>\n')
self.response.write('<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">\n')
self.response.write('<style type="text/css">\n')
self.response.write('table {width:0%; border-width:1px; padding: 0;border-collapse: collapse;}\n')
self.response.write('table tr {border-top: 1px solid #b8b8b8; background-color: white; margin: 0; padding: 0;}\n')
self.response.write('table tr:nth-child(2n) {background-color: #f8f8f8;}\n')
self.response.write('table thead tr :last-child {width:100%;}\n')
self.response.write('table tr th {font-weight: bold; border: 1px solid #b8b8b8; background-color: #cdcdcd; margin: 0; padding: 6px 13px;}\n')
self.response.write('table tr th {font-weight: bold; border: 1px solid #b8b8b8; background-color: #cdcdcd; margin: 0; padding: 6px 13px;}\n')
self.response.write('table tr td {border: 1px solid #b8b8b8; margin: 0; padding: 6px 13px;}\n')
self.response.write('table tr th :first-child, table tr td :first-child {margin-top: 0;}\n')
self.response.write('table tr th :last-child, table tr td :last-child {margin-bottom: 0;}\n')
self.response.write('</style>\n')
self.response.write('</head>\n')
self.response.write('<body style="min-width:900px">\n')
if self.debug and not self.request.get('user', None):
self.response.write('<form name="username" action="" method="get">\n')
self.response.write('Username: <input type="text" name="user">\n')
self.response.write('<input type="submit" value="Generate Custom Links">\n')
self.response.write('</form>\n')
self.response.write(markdown.markdown(resources, ['extra']))
self.response.write('</body>\n')
self.response.write('</html>\n')
def put(self):
# TODO add security: either authenticated user or machine-to-machine CRAM
if 'Content-MD5' not in self.request.headers:
self.abort(400, 'Request must contain a valid "Content-MD5" header.')
filename = self.request.get('filename', 'upload')
with tempfile.TemporaryDirectory(prefix='.tmp', dir=self.app.config['store_path']) as tempdir_path:
hash_ = hashlib.sha1()
filepath = os.path.join(tempdir_path, filename)
with open(filepath, 'wb') as fd:
for chunk in iter(lambda: self.request.body_file.read(2**20), ''):
hash_.update(chunk)
fd.write(chunk)
if hash_.hexdigest() != self.request.headers['Content-MD5']:
self.abort(400, 'Content-MD5 mismatch.')
if not tarfile.is_tarfile(filepath):
self.abort(415, 'Only tar files are accepted.')
log.info('Received %s [%s] from %s' % (filename, hrsize(self.request.content_length), self.request.user_agent))
status, detail = sort_file(self.app.db, filepath, hash_.hexdigest(), self.app.config['store_path'])
if status != 200:
self.abort(status, detail)
def download(self):
if self.request.method == 'OPTIONS':
return self.options()
paths = []
symlinks = []
for js_id in self.request.get('id', allow_multiple=True):
type_, _id = js_id.split('_')
_idpaths, _idsymlinks = resource_types[type_].download_info(_id)
paths += _idpaths
symlinks += _idsymlinks
def login(self):
"""Return details for the current User."""
if self.request.method == 'OPTIONS':
return self.options()
log.debug(self.uid + ' has logged in')
return self.app.db.users.find_and_modify({'_id': self.uid}, {'$inc': {'logins': 1}}, fields=['firstname', 'lastname', 'superuser'])
def sites(self):
"""Return local and remote sites."""
if self.request.method == 'OPTIONS':
return self.options()
if self.request.get('all').lower() in ('1', 'true'):
remotes = list(self.app.db.remotes.find(None, ['name']))
else:
remotes = (self.app.db.users.find_one({'_id': self.uid}, ['remotes']) or {}).get('remotes', [])
return dict(local={'_id': self.app.config['site_id'], 'name': self.app.config['site_name']}, remotes=remotes)
def roles(self):
"""Return the list of user roles."""
if self.request.method == 'OPTIONS':
return self.options()
return base.ROLES
def log(self):
"""Return logs."""
if self.request.method == 'OPTIONS':
return self.options()
try:
logs = open(self.app.config['log_path']).readlines()
except IOError as e:
if 'Permission denied' in e:
body_template = '${explanation}<br /><br />${detail}<br /><br />${comment}'
comment = 'To fix permissions, run the following command: chmod o+r ' + self.app.config['log_path']
self.abort(500, detail=str(e), comment=comment, body_template=body_template)
else: # file does not exist
self.abort(500, 'log_path variable misconfigured or not set')
try:
n = int(self.request.get('n', 10000))
except:
self.abort(400, 'n must be an integer')
return [line.strip() for line in reversed(logs) if re.match('[-:0-9 ]{18} +nimsapi:(?!.*[/a-z]*/log )', line)][:n]
search_schema = {
'title': 'Search',
'type': 'array',
'items': [
{
'title': 'Session',
'type': 'array',
'items': [
{
'title': 'Date',
'type': 'date',
'field': 'session.date',
},
{
'title': 'Subject',
'type': 'array',
'items': [
{
'title': 'Name',
'type': 'array',
'items': [
{
'title': 'First',
'type': 'string',
'field': 'session.subject.firstname',
},
{
'title': 'Last',
'type': 'string',
'field': 'session.subject.lastname',
},
],
},
{
'title': 'Date of Birth',
'type': 'date',
'field': 'session.subject.dob',
},
{
'title': 'Sex',
'type': 'string',
'enum': ['male', 'female'],
'field': 'session.subject.sex',
},
],
},
],
},
{
'title': 'MR',
'type': 'array',
'items': [
{
'title': 'Scan Type',
'type': 'string',
'enum': ['anatomical', 'fMRI', 'DTI'],
'field': 'acquisition.type',
},
{
'title': 'Echo Time',
'type': 'number',
'field': 'acquisition.echo_time',
},
{
'title': 'Size',
'type': 'array',
'items': [
{
'title': 'X',
'type': 'integer',
'field': 'acquisition.size.x',
},
{
'title': 'Y',
'type': 'integer',
'field': 'acquisition.size.y',
},
],
},
],
},
{
'title': 'EEG',
'type': 'array',
'items': [
{
'title': 'Electrode Count',
'type': 'integer',
'field': 'acquisition.electrode_count',
},
],
},
],
}
def search(self):
"""Search."""
if self.request.method == 'OPTIONS':
return self.options()
elif self.request.method == 'GET':
return self.search_schema
else:
pass