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# @author: Gunnar Schaefer, Kevin S. Hahn
import logging
log = logging.getLogger('nimsapi')
import os
import re
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')
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/users)] | list of users
[(nimsapi/users/count)] | count of users
[(nimsapi/users/listschema)] | schema for user list
[(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/listschema)] | schema for group list
[(nimsapi/groups/schema)] | schema for single group
nimsapi/groups/*<gid>* | details for group *<gid>*
[(nimsapi/experiments)] | list of experiments
[(nimsapi/experiments/count)] | count of experiments
[(nimsapi/experiments/listschema)] | schema for experiment list
[(nimsapi/experiments/schema)] | schema for single experiment
nimsapi/experiments/*<xid>* | details for experiment *<xid>*
nimsapi/experiments/*<xid>*/sessions | list sessions for experiment *<xid>*
[(nimsapi/sessions/count)] | count of sessions
[(nimsapi/sessions/listschema)] | schema for sessions list
[(nimsapi/sessions/schema)] | schema for single session
nimsapi/sessions/*<sid>* | details for session *<sid>*
nimsapi/sessions/*<sid>*/move | move session *<sid>* to a different experiment
nimsapi/sessions/*<sid>*/epochs | list epochs for session *<sid>*
[(nimsapi/epochs/count)] | count of epochs
[(nimsapi/epochs/listschema)] | schema for epoch list
[(nimsapi/epochs/schema)] | schema for single epoch
nimsapi/epochs/*<eid>* | details for epoch *<eid>*
[(nimsapi/collections)] | list of collections
[(nimsapi/collections/count)] | count of collections
[(nimsapi/collections/listschema)] | schema for collections list
[(nimsapi/collections/schema)] | schema for single collection
nimsapi/collections/*<cid>* | details for collection *<cid>*
nimsapi/collections/*<cid>*/sessions | list sessions for collection *<cid>*
nimsapi/collections/*<cid>*/epochs?session=*<sid>* | list of epochs for collection *<cid>*, optionally restricted to session *<sid>*
"""
resources = re.sub(r'\[\((.*)\)\]', r'[\1](\1)', 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')
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', 'anonymous')
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))
try:
log.info('Parsing %s' % filename)
dataset = nimsdata.parse(filepath)
except nimsdata.NIMSDataError:
self.abort(415, 'Can\'t parse %s' % filename)
else:
log.info('Sorting %s' % filename)
# TODO: bail, if any required params are not set
epoch_spec, epoch_id = self.update_db(dataset)
epoch_path = os.path.join(self.app.config['store_path'], epoch_id[-3:] + '/' + epoch_id)
if not os.path.exists(epoch_path):
os.makedirs(epoch_path)
file_ext = '.' + filename.split('.', 1)[1] # split on the first .
file_spec = dict(epoch_spec.items() + [('files.datatype', dataset.nims_type)])
file_info = dict(
datatype=dataset.nims_type,
filename=dataset.nims_filename,
ext=file_ext,
size=os.path.getsize(filepath),
sha1=hash_.hexdigest(),
#hash=dataset.nims_hash, TODO: datasets should be able to hash themselves (but not here)
)
success = self.app.db.epochs.update(file_spec, {'$set': {'files.$': file_info}})
if not success['updatedExisting']:
self.app.db.epochs.update(epoch_spec, {'$addToSet': {'files': file_info}})
shutil.move(filepath, epoch_path + '/' + dataset.nims_filename + file_ext)
log.debug('Done %s' % filename)
def update_db(self, dataset):
existing_group_names = [g['_id'] for g in self.app.db.groups.find(None, ['_id'])]
group_name_matches = difflib.get_close_matches(dataset.nims_group, existing_group_names, cutoff=0.8)
if len(group_name_matches) == 1:
group_name = group_name_matches[0]
experiment_name = dataset.nims_experiment or 'untitled'
else:
group_name = 'unknown'
experiment_name = group_name + '/' + dataset.nims_experiment
group = self.app.db.groups.find_one({'_id': group_name})
experiment_spec = {'group': group['_id'], 'name': experiment_name}
experiment = self.app.db.experiments.find_and_modify(
experiment_spec,
{'$setOnInsert': dict(permissions=group['roles'], files=[])},
upsert=True,
new=True,
)
# experiment timestamp and timezone are inherited from latest epoch
if experiment.get('timestamp', dataset.nims_timestamp - datetime.timedelta(1)) < dataset.nims_timestamp:
self.app.db.experiments.update(experiment_spec, {'$set': dict(timestamp=dataset.nims_timestamp, timezone=dataset.nims_timezone)})
session_spec = {'uid': dataset.nims_session}
session = self.app.db.sessions.find_and_modify(
session_spec,
{
'$setOnInsert': dict(experiment=experiment['_id'], files=[]),
'$set': self.entity_metadata(dataset, dataset.session_properties, session_spec), # session_spec ensures non-empty $set
},
upsert=True,
new=True,
)
# session timestamp and timezone are inherited from earliest epoch
if session.get('timestamp', dataset.nims_timestamp + datetime.timedelta(1)) > dataset.nims_timestamp:
self.app.db.sessions.update(session_spec, {'$set': dict(timestamp=dataset.nims_timestamp, timezone=dataset.nims_timezone)})
epoch_spec = {'uid': dataset.nims_epoch}
epoch = self.app.db.epochs.find_and_modify(
epoch_spec,
{
'$setOnInsert': dict(session=session['_id'], files=[]),
'$set': self.entity_metadata(dataset, dataset.epoch_properties),
},
upsert=True,
new=True,
)
return epoch_spec, str(epoch['_id'])
@staticmethod
def entity_metadata(dataset, properties, presets={}):
metadata = [(prop, getattr(dataset, attrs['attribute'])) for prop, attrs in properties.iteritems() if 'attribute' in attrs]
return {key: value for key, value in (metadata + presets.items()) if value is not None}
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}, {'$inc': {'logins': 1}}, fields=['firstname', 'lastname', 'superuser'])
def sites(self):
"""Return local and remote sites."""
if self.request.method == 'OPTIONS':
return self.options()
return dict(
local={'_id': self.app.config['site_id'], 'name': self.app.config['site_name']},
remotes=list(self.app.db.remotes.find(None, ['name'])),
)
def roles(self):
"""Return the list of user roles."""
if self.request.method == 'OPTIONS':
return self.options()
return base.ROLES
def log(self):
"""Return logs."""
if self.request.method == 'OPTIONS':
return self.options()
try:
logs = open(self.app.config['log_path']).readlines()
except IOError as e:
if 'Permission denied' in e:
body_template = '${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]