def index(self, ordered=False):
"""
Get all plugins available
@param ordered: if you want a nested json based on
plugins paths
"""
user = util.get_user(tg.request)
if user.is_service:
d = {'plugins': putil.get_plugins_path(service=user, ordered=ordered)}
else:
d = {'plugins': putil.get_plugins_path(ordered=ordered)}
return d
def wrapped(self, *args, **kw):
user = util.get_user(request)
conn = model.Connection()
conn.user_id = user.id
conn.ip = request.remote_addr
conn.user_agent = request.user_agent
conn.url = request.url
conn.method = request.method
conn.content_length = request.content_length
conn.content_type = request.content_type
conn.query_string = request.query_string
conn.body = ','.join(['%s:%s' % (k, v) for k, v in request.params.iteritems()])
model.DBSession.add(conn)
return fn(self, *args, **kw)
def wrapped(self, *args, **kw):
user = util.get_user(request)
conn = model.Connection()
conn.user_id = user.id
conn.ip = request.remote_addr
conn.user_agent = request.user_agent
conn.url = request.url
conn.method = request.method
conn.content_length = request.content_length
conn.content_type = request.content_type
conn.query_string = request.query_string
conn.body = ','.join(
['%s:%s' % (k, v) for k, v in request.params.iteritems()])
model.DBSession.add(conn)
return fn(self, *args, **kw)
def index(self, ordered=False):
"""
Get all plugins available
@param ordered: if you want a nested json based on
plugins paths
"""
user = util.get_user(tg.request)
if user.is_service:
d = {
'plugins':
operations.get_plugins_path(service=user, ordered=ordered)
}
else:
d = {'plugins': operations.get_plugins_path(ordered=ordered)}
return d
def get(self, id, *args, **kw):
"""
Display the form by it's id
"""
# check plugin id
plug = None
try:
plug = putil.get_plugin_byId(id)
except:
tg.abort(400, "Bad plugin identifier")
debug('get plugin %s' % id)
# get the plugin
obj = plug
info = obj.info
form = info.get('output')()
desc = info.get('description')
debug('params = %s' % kw, 1)
# bioscript parameters
bs_private = {}
if 'bs_private' in kw:
bs_private = json.loads(kw['bs_private'])
debug("get bs private parameters %s" % bs_private, 2)
if 'prefill' in bs_private:
prefill_fields(info.get('in'), form, bs_private['prefill'], kw)
# {'bs_private': {'app': pp, 'cfg': handler.job.bioscript_config, 'prefill': prefill}})
# add some private parameters from BioScript
pp = {'id': id}
# if user is a serviec, add the key & the mail in the authentication
user = util.get_user(tg.request)
if user.is_service:
pp['mail'] = user.email
pp['key'] = user.key
bs_private['pp'] = pp
# prepare form output
main_proxy = tg.config.get('main.proxy')
widget = form(action=main_proxy + tg.url('/plugins/validate', {'id': id})).req()
widget.value = {'bs_private': json.dumps(bs_private), 'key': user.key}
debug('display plugin with bs_private : %s' % bs_private)
debug('vaaalue : %s' % widget.value)
debug(user)
return {'page': 'plugin', 'desc': desc, 'title': info.get('title'), 'widget': widget}
def validate(self, **kw):
"""
plugin parameters validation
"""
user = util.get_user(tg.request)
debug('Got request validation from user %s' % user)
if not 'bs_private' in kw:
tg.abort(400, "Plugin identifier not found in the request.")
debug('params %s' % kw, 1)
bs_private = copy.deepcopy(json.loads(kw['bs_private']))
debug('private %s' % bs_private, 1)
plugin_id = bs_private['pp']['id']
if plugin_id is None:
tg.abort(400, "Plugin identifier not found in the request.")
# check plugin id
plug = putil.get_plugin_byId(plugin_id)
if plug is None:
tg.abort(400, "Bad plugin identifier")
# get plugin form output
obj = plug
info = obj.info
form = info.get('output')()
# callback for jsonP
callback = kw.get('callback', 'callback')
# get the plugin from the database
plugin_db = DBSession.query(Plugin).filter(Plugin.generated_id == obj.unique_id()).first()
plugin_request = _log_form_request(plugin_id=plugin_db.id, user=user, parameters=kw)
if 'prefill' in bs_private:
prefill_fields(info.get('in'), form, bs_private['prefill'], kw, replace_value=False)
debug('prefill in validation', 3)
del bs_private['prefill']
# validation
try:
form = form().req()
form.validate(kw)
except (tw2.core.ValidationError, Invalid) as e:
main_proxy = tg.config.get('main.proxy')
e.widget.action = main_proxy + tg.url('plugins/index', {'id': plugin_id})
debug('private after validation failed %s' % bs_private, 1)
#value = {'bs_private': json.dumps(bs_private)}
#debug('value %s' % value)
#e.widget.value = value
plugin_request.status = 'FAILED'
plugin_request.error = str(e)
DBSession.add(plugin_request)
return jsonp_response(**{'validation': 'failed', 'desc': info.get('description'),
'title': info.get('title'), 'widget': e.widget.display(), 'callback': callback})
debug('Validation pass')
#if the validation passes, remove private parameters from the request
del kw['bs_private']
if 'key' in kw:
del kw['key']
# fetch form files
try:
inputs_directory = filemanager.fetch(user, obj, kw)
except Exception as e:
plugin_request.status = 'FAILED'
plugin_request.error = str(e)
DBSession.add(plugin_request)
import sys
import traceback
etype, value, tb = sys.exc_info()
traceback.print_exception(etype, value, tb)
return jsonp_response(**{'validation': 'success', 'desc': info.get('description'),
'title': info.get('title'), 'error': 'error while fetching files : ' + str(e), 'callback': callback})
debug('Files fetched')
# get output directory to write results
outputs_directory = filemanager.temporary_directory(constants.paths['data'])
service_callback = None
debug(user)
if user.is_service:
debug('is service', 1)
# def out_path(service_name):
o = services.service_manager.get(user.name, constants.SERVICE_RESULT_ROOT_PARAMETER)
if o:
outputs_directory = o
service_callback = services.service_manager.get(user.name, constants.SERVICE_CALLBACK_URL_PARAMETER)
debug('Output dir = %s' % outputs_directory)
# get user parameters from the request
user_parameters = bs_private.get('app', "{}")
debug('get user parameters : %s' % user_parameters, 1)
# get response config from the request
resp_config = bs_private.get('cfg', None)
plugin_info = {'title': info['title'],
'plugin_id': plugin_db.id,
'generated_id': plugin_db.generated_id,
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']}
# call plugin process
bioscript_callback = tg.config.get('main.proxy') + '/' + tg.url('plugins/callback_results')
async_res = tasks.plugin_job.delay(user.name, inputs_directory, outputs_directory, plugin_info,
user_parameters, service_callback, bioscript_callback, **kw)
task_id = async_res.task_id
_log_job_request(plugin_request.id, task_id)
if resp_config and resp_config.get('plugin_info', '') == 'min':
return jsonp_response(**{'validation': 'success', 'plugin_id': plugin_id, 'task_id': task_id, 'callback': callback, 'app': user_parameters})
return jsonp_response(**{
'validation': 'success',
'plugin_id': plugin_id,
'task_id': task_id,
'plugin_info': json.dumps(
{'title': info['title'],
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']}),
'callback': callback, 'app': user_parameters})
def fetch(self, oid, *args, **kw):
"""
Display the form by it's id
"""
debug('\n[plugin controller]FETCH')
# check plugin id
plug = None
try:
plug = operations.get_plugin_byId(oid)
except:
tg.abort(400, "Bad plugin identifier")
debug('[x] get plugin %s' % oid,)
# get the plugin
obj = plug
info = obj.info
form = info.get('output')()
desc = plug.description_as_html
debug('[x] params = %s' % kw,)
# bioscript parameters
bs_private = {}
if 'bs_private' in kw:
bs_private = json.loads(kw['bs_private'])
debug("[x] get bs private parameters %s" % bs_private,)
if 'prefill' in bs_private:
prefill_fields(info.get('in'), form, bs_private['prefill'], kw)
# add some private parameters from BioScript
pp = {'id': oid}
# if user is a service, add the key & the mail in the authentication
user = util.get_user(tg.request)
if user.is_service:
pp['mail'] = user.email
pp['key'] = user.key
bs_private['pp'] = pp
# prepare form output
main_proxy = tg.config.get('main.proxy')
widget = form(action=main_proxy + tg.url('/plugins/validate', {'id': oid})).req()
widget.value = {'bs_private': json.dumps(bs_private), 'key': user.key}
debug('display plugin with bs_private : %s' % bs_private)
debug('vaaalue : %s' % widget.value)
debug(user)
debug('END FETCH')
html_doc = ''
html_src_code = ''
try:
html_doc = obj.html_doc_link()
html_src_code = obj.html_source_code_link()
except Exception as e:
print '"html_doc" and "src_code" seems to be missing for your plugin, please update bsplugins to the last version'
print e
meta = info.get('meta', {})
return {'page': 'plugin',
'desc': desc,
'title': info.get('title'),
'widget': widget,
'html_doc': html_doc,
'html_src_code': html_src_code,
'author': meta.get('author'),
'contact': meta.get('contact')}
def validate(self, **kw):
"""
plugin parameters validation
"""
user = util.get_user(tg.request)
# get private bioscript parameters
if not 'bs_private' in kw:
debug('bs_private not found')
tg.abort(400, "Plugin identifier not found in the request.")
bs_private = copy.deepcopy(json.loads(kw['bs_private']))
debug('\n[plugin controller]\nVALIDATE %s' % kw,)
# get the plugin from the private parameters
plugin_id = 0
try:
plugin_id = bs_private['pp']['id']
except KeyError:
tg.abort(400, "Plugin identifier not found in the request.")
if plugin_id == 0:
tg.abort(400, "Plugin identifier not found in the request.")
plug = operations.get_plugin_byId(plugin_id)
if plug is None:
tg.abort(400, "Bad plugin identifier.")
# get the plugin from database
plugin_db = DBSession.query(Plugin).filter(Plugin.generated_id == plug.unique_id()).first()
# validate the form
# we must do an HTTP call because I don't find a way
# to call the 'render' method on 'plugin_validate' template
request_url = tg.config.get('main.proxy') + '/plugins/_validate'
validated = True
info = plug.info
# get the callback if any
callback = kw.get('callback', 'callback')
try:
form = urllib2.urlopen(request_url, urllib.urlencode(kw)).read()
# add some header because the request can come from another domain
response.headers['Access-Control-Allow-Headers'] = 'X-CSRF-Token'
response.headers['Access-Control-Allow-Origin'] = '*'
try:
form = json.loads(form)
except:
pass
validated = isinstance(form, dict)
except Exception as e:
util.print_traceback()
validated = False
form = 'Problem with Bioscript server.'
if not validated:
debug('Validation failed',)
return json.dumps({'validation': 'failed',
'desc': info.get('description'),
'title': info.get('title'),
'widget': form,
'callback': callback})
# validation passes
new_params = form['params']
new_params = kw
debug('Validation passes with params : %s' % new_params,)
# we regoup all multi stuff in a single list:
# for instance a multi field will give parameters like:
# {SigMulti:1:signals: val1, SigMulti:2:signals: val2, ...}
# and we will transform it to
# {SigMulti: { signals : [val1, val2], ...}
grouped_params = {}
todel = []
for k, v in new_params.iteritems():
m = multipattern.match(k)
if m is not None:
todel.append(k)
if v or isinstance(v, cgi.FieldStorage):
key1, n, key2 = m.groups()
if key1 not in grouped_params:
grouped_params[key1] = {}
if key2 in grouped_params[key1]:
grouped_params[key1][key2][int(n) - 1] = v
elif not key2.endswith('bs_group'):
sl = SparseList()
sl[int(n) - 1] = v
grouped_params[key1][key2] = sl
debug('group "multi" params: %s' % grouped_params)
# debug('check fieldstorages',)
# # must keep fieldstorages because they were converted to str
# fs_bk = []
# import cgi
# for k, v in kw.iteritems():
# if isinstance(v, cgi.FieldStorage):
# fs_bk.append((k, v))
# debug(fs_bk)
# for fsk, fsv in fs_bk:
# m = multipattern.match(fsk)
# if m:
# key1, n, key2 = m.groups()
# grouped_params[key1][key2][int(n) - 1] = fsv
# else:
# grouped_params[fsk] = fsv
new_params.update(grouped_params)
# delete multi parameters
for td in todel:
del new_params[td]
# but we need to keep all params that are multi and urls
kw = new_params
#remove private parameters from the request
if 'bs_private' in kw:
del kw['bs_private']
if 'key' in kw:
del kw['key']
debug('New params are : %s' % new_params,)
# update plugin arameters
# log the request, it's a valid one
plugin_request = _log_form_request(plugin_id=plugin_db.id, user=user, parameters=dict(kw))
DBSession.add(plugin_request)
debug('get output directory',)
# get output directory to write results
outputs_directory = filemanager.temporary_directory(constants.paths['data'])
service_callback = None
# if the user is a service, get parameters from configuration
if user.is_service:
debug('is service',)
o = services.service_manager.get(user.name, constants.SERVICE_RESULT_ROOT_PARAMETER)
if o:
outputs_directory = o
service_callback = services.service_manager.get(user.name, constants.SERVICE_CALLBACK_URL_PARAMETER)
debug('Write result in %s' % outputs_directory,)
# get prvate parameters from the request
private_parameters = bs_private.get('app', "{}")
# get response configuration from the request
resp_config = bs_private.get('cfg', None)
plugin_info = {'title': info['title'],
'plugin_id': plugin_db.id,
'generated_id': plugin_db.generated_id,
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']}
# define the bioscript callback
bioscript_callback = tg.config.get('main.proxy') + '/' + tg.url('plugins/callback_results')
debug("callback on bs : %s " % bioscript_callback,)
# if some files come from a file field, we must download them directly
inputs_directory, dwdfiles = filemanager.fetchfilefields(user, plug, kw)
# chain jobs : fetch files then plugin process
async_res = tasks.plugin_job.delay(user,
plug,
inputs_directory,
outputs_directory,
dwdfiles,
plugin_info,
private_parameters,
service_callback,
bioscript_callback,
**kw)
task_id = async_res.task_id
debug('Launch task %s' % task_id,)
# log the job request
_log_job_request(plugin_request.id, task_id)
#prepare the response
resp = {'validation': 'success',
'plugin_id': plugin_id,
'task_id': task_id,
'callback': callback,
'app': private_parameters}
if resp_config and resp_config.get('plugin_info', '') == 'min':
resp.update({'plugin_info': json.dumps({'title': info['title'],
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']})})
return json.dumps(resp)
def fetch(self, oid, *args, **kw):
"""
Display the form by it's id
"""
debug('\n[plugin controller]FETCH')
# check plugin id
plug = None
try:
plug = operations.get_plugin_byId(oid)
except:
tg.abort(400, "Bad plugin identifier")
debug('[x] get plugin %s' % oid, )
# get the plugin
obj = plug
info = obj.info
form = info.get('output')()
desc = plug.description_as_html
debug('[x] params = %s' % kw, )
# bioscript parameters
bs_private = {}
if 'bs_private' in kw:
bs_private = json.loads(kw['bs_private'])
debug("[x] get bs private parameters %s" % bs_private, )
if 'prefill' in bs_private:
prefill_fields(info.get('in'), form, bs_private['prefill'], kw)
# add some private parameters from BioScript
pp = {'id': oid}
# if user is a service, add the key & the mail in the authentication
user = util.get_user(tg.request)
if user.is_service:
pp['mail'] = user.email
pp['key'] = user.key
bs_private['pp'] = pp
# prepare form output
main_proxy = tg.config.get('main.proxy')
widget = form(action=main_proxy +
tg.url('/plugins/validate', {'id': oid})).req()
widget.value = {'bs_private': json.dumps(bs_private), 'key': user.key}
debug('display plugin with bs_private : %s' % bs_private)
debug('vaaalue : %s' % widget.value)
debug(user)
debug('END FETCH')
html_doc = ''
html_src_code = ''
try:
html_doc = obj.html_doc_link()
html_src_code = obj.html_source_code_link()
except Exception as e:
print '"html_doc" and "src_code" seems to be missing for your plugin, please update bsplugins to the last version'
print e
meta = info.get('meta', {})
return {
'page': 'plugin',
'desc': desc,
'title': info.get('title'),
'widget': widget,
'html_doc': html_doc,
'html_src_code': html_src_code,
'author': meta.get('author'),
'contact': meta.get('contact')
}
def validate(self, **kw):
"""
plugin parameters validation
"""
user = util.get_user(tg.request)
# get private bioscript parameters
if not 'bs_private' in kw:
debug('bs_private not found')
tg.abort(400, "Plugin identifier not found in the request.")
bs_private = copy.deepcopy(json.loads(kw['bs_private']))
debug('\n[plugin controller]\nVALIDATE %s' % kw, )
# get the plugin from the private parameters
plugin_id = 0
try:
plugin_id = bs_private['pp']['id']
except KeyError:
tg.abort(400, "Plugin identifier not found in the request.")
if plugin_id == 0:
tg.abort(400, "Plugin identifier not found in the request.")
plug = operations.get_plugin_byId(plugin_id)
if plug is None:
tg.abort(400, "Bad plugin identifier.")
# get the plugin from database
plugin_db = DBSession.query(Plugin).filter(
Plugin.generated_id == plug.unique_id()).first()
# validate the form
# we must do an HTTP call because I don't find a way
# to call the 'render' method on 'plugin_validate' template
request_url = tg.config.get('main.proxy') + '/plugins/_validate'
validated = True
info = plug.info
# get the callback if any
callback = kw.get('callback', 'callback')
try:
form = urllib2.urlopen(request_url, urllib.urlencode(kw)).read()
# add some header because the request can come from another domain
response.headers['Access-Control-Allow-Headers'] = 'X-CSRF-Token'
response.headers['Access-Control-Allow-Origin'] = '*'
try:
form = json.loads(form)
except:
pass
validated = isinstance(form, dict)
except Exception as e:
util.print_traceback()
validated = False
form = 'Problem with Bioscript server.'
if not validated:
debug('Validation failed', )
return json.dumps({
'validation': 'failed',
'desc': info.get('description'),
'title': info.get('title'),
'widget': form,
'callback': callback
})
# validation passes
new_params = form['params']
new_params = kw
debug('Validation passes with params : %s' % new_params, )
# we regoup all multi stuff in a single list:
# for instance a multi field will give parameters like:
# {SigMulti:1:signals: val1, SigMulti:2:signals: val2, ...}
# and we will transform it to
# {SigMulti: { signals : [val1, val2], ...}
grouped_params = {}
todel = []
for k, v in new_params.iteritems():
m = multipattern.match(k)
if m is not None:
todel.append(k)
if v or isinstance(v, cgi.FieldStorage):
key1, n, key2 = m.groups()
if key1 not in grouped_params:
grouped_params[key1] = {}
if key2 in grouped_params[key1]:
grouped_params[key1][key2][int(n) - 1] = v
elif not key2.endswith('bs_group'):
sl = SparseList()
sl[int(n) - 1] = v
grouped_params[key1][key2] = sl
debug('group "multi" params: %s' % grouped_params)
# debug('check fieldstorages',)
# # must keep fieldstorages because they were converted to str
# fs_bk = []
# import cgi
# for k, v in kw.iteritems():
# if isinstance(v, cgi.FieldStorage):
# fs_bk.append((k, v))
# debug(fs_bk)
# for fsk, fsv in fs_bk:
# m = multipattern.match(fsk)
# if m:
# key1, n, key2 = m.groups()
# grouped_params[key1][key2][int(n) - 1] = fsv
# else:
# grouped_params[fsk] = fsv
new_params.update(grouped_params)
# delete multi parameters
for td in todel:
del new_params[td]
# but we need to keep all params that are multi and urls
kw = new_params
#remove private parameters from the request
if 'bs_private' in kw:
del kw['bs_private']
if 'key' in kw:
del kw['key']
debug('New params are : %s' % new_params, )
# update plugin arameters
# log the request, it's a valid one
plugin_request = _log_form_request(plugin_id=plugin_db.id,
user=user,
parameters=dict(kw))
DBSession.add(plugin_request)
debug('get output directory', )
# get output directory to write results
outputs_directory = filemanager.temporary_directory(
constants.paths['data'])
service_callback = None
# if the user is a service, get parameters from configuration
if user.is_service:
debug('is service', )
o = services.service_manager.get(
user.name, constants.SERVICE_RESULT_ROOT_PARAMETER)
if o:
outputs_directory = o
service_callback = services.service_manager.get(
user.name, constants.SERVICE_CALLBACK_URL_PARAMETER)
debug('Write result in %s' % outputs_directory, )
# get prvate parameters from the request
private_parameters = bs_private.get('app', "{}")
# get response configuration from the request
resp_config = bs_private.get('cfg', None)
plugin_info = {
'title': info['title'],
'plugin_id': plugin_db.id,
'generated_id': plugin_db.generated_id,
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']
}
# define the bioscript callback
bioscript_callback = tg.config.get('main.proxy') + '/' + tg.url(
'plugins/callback_results')
debug("callback on bs : %s " % bioscript_callback, )
# if some files come from a file field, we must download them directly
inputs_directory, dwdfiles = filemanager.fetchfilefields(
user, plug, kw)
# chain jobs : fetch files then plugin process
async_res = tasks.plugin_job.delay(user, plug, inputs_directory,
outputs_directory, dwdfiles,
plugin_info, private_parameters,
service_callback,
bioscript_callback, **kw)
task_id = async_res.task_id
debug('Launch task %s' % task_id, )
# log the job request
_log_job_request(plugin_request.id, task_id)
#prepare the response
resp = {
'validation': 'success',
'plugin_id': plugin_id,
'task_id': task_id,
'callback': callback,
'app': private_parameters
}
if resp_config and resp_config.get('plugin_info', '') == 'min':
resp.update({
'plugin_info':
json.dumps({
'title': info['title'],
'description': info['description'],
'path': info['path'],
'in': info['in'],
'out': info['out'],
'meta': info['meta']
})
})
return json.dumps(resp)