def own_handle(self, genome, handle_property, ctx):
if not handle_property in genome:
return
token = ctx['token']
handle_id = genome[handle_property]
hs = HandleService(self.handle_url, token=token)
handles = hs.hids_to_handles([handle_id])
shock_id = handles[0]['id']
## Copy from DataFileUtil.own_shock_node implementation:
header = {'Authorization': 'Oauth {}'.format(token)}
res = requests.get(self.shock_url + '/node/' + shock_id +
'/acl/?verbosity=full',
headers=header, allow_redirects=True)
self.check_shock_response(
res, 'Error getting ACLs for Shock node {}: '.format(shock_id))
owner = res.json()['data']['owner']['username']
if owner != ctx['user_id']:
shock_id = self.copy_shock_node(ctx, shock_id)
r = requests.get(self.shock_url + '/node/' + shock_id,
headers=header, allow_redirects=True)
errtxt = ('Error downloading attributes from shock ' +
'node {}: ').format(shock_id)
self.check_shock_response(r, errtxt)
shock_data = r.json()['data']
handle = {'id': shock_data['id'],
'type': 'shock',
'url': self.shock_url,
'file_name': shock_data['file']['name'],
'remote_md5': shock_data['file']['checksum']['md5']
}
handle_id = hs.persist_handle(handle)
genome[handle_property] = handle_id
def own_handle(self, genome, handle_property, ctx):
if not handle_property in genome:
return
token = ctx['token']
handle_id = genome[handle_property]
hs = HandleService(self.handle_url, token=token)
handles = hs.hids_to_handles([handle_id])
shock_id = handles[0]['id']
## Copy from DataFileUtil.own_shock_node implementation:
header = {'Authorization': 'Oauth {}'.format(token)}
res = requests.get(self.shock_url + '/node/' + shock_id +
'/acl/?verbosity=full',
headers=header,
allow_redirects=True)
self.check_shock_response(
res, 'Error getting ACLs for Shock node {}: '.format(shock_id))
owner = res.json()['data']['owner']['username']
if owner != ctx['user_id']:
shock_id = self.copy_shock_node(ctx, shock_id)
r = requests.get(self.shock_url + '/node/' + shock_id,
headers=header,
allow_redirects=True)
errtxt = ('Error downloading attributes from shock ' +
'node {}: ').format(shock_id)
self.check_shock_response(r, errtxt)
shock_data = r.json()['data']
handle = {
'id': shock_data['id'],
'type': 'shock',
'url': self.shock_url,
'file_name': shock_data['file']['name'],
'remote_md5': shock_data['file']['checksum']['md5']
}
handle_id = hs.persist_handle(handle)
genome[handle_property] = handle_id
def getPairedEndLibInfo(self):
if hasattr(self.__class__, 'pairedEndLibInfo'):
return self.__class__.pairedEndLibInfo
# 1) upload files to shock
token = self.ctx['token']
forward_shock_file = self.upload_file_to_shock(
shock_service_url=self.shockURL,
filePath='data/small.forward.fq',
token=token)
reverse_shock_file = self.upload_file_to_shock(
shock_service_url=self.shockURL,
filePath='data/small.reverse.fq',
token=token)
pprint(forward_shock_file)
pprint(reverse_shock_file)
# 2) create handle
hs = HandleService(url=self.handleURL, token=token)
handf = {
'id': forward_shock_file['id'],
'type': 'shock',
'url': self.shockURL,
'file_name': forward_shock_file['file']['name'],
'remote_md5': forward_shock_file['file']['checksum']['md5']
}
forward_handle = hs.persist_handle(handf)
handr = {
'id': reverse_shock_file['id'],
'type': 'shock',
'url': self.shockURL,
'file_name': reverse_shock_file['file']['name'],
'remote_md5': reverse_shock_file['file']['checksum']['md5']
}
reverse_handle = hs.persist_handle(handr)
# 3) save to WS
paired_end_library = {
'lib1': {
'file': {
'hid': forward_handle,
'file_name': forward_shock_file['file']['name'],
'id': forward_shock_file['id'],
'url': self.shockURL,
'type': 'shock',
'remote_md5': forward_shock_file['file']['checksum']['md5']
},
'encoding': 'UTF8',
'type': 'fastq',
'size': forward_shock_file['file']['size']
},
'lib2': {
'file': {
'hid': reverse_handle,
'file_name': reverse_shock_file['file']['name'],
'id': reverse_shock_file['id'],
'url': self.shockURL,
'type': 'shock',
'remote_md5': reverse_shock_file['file']['checksum']['md5']
},
'encoding': 'UTF8',
'type': 'fastq',
'size': reverse_shock_file['file']['size']
},
'interleaved': 0,
'sequencing_tech': 'artificial reads',
'read_length_mean': 100,
'insert_size_mean': 250,
'insert_size_std_dev': 10,
'total_bases': 125000,
'read_orientation_outward': 1
}
ws_obj = {
'workspace': self.getWsName(),
'objects': [
{
'type': 'KBaseFile.PairedEndLibrary',
'data': paired_end_library,
'name': 'test.pe.reads',
'meta': {},
'provenance': [
{
'service': 'hipmer',
'method': 'test_hipmer'
}
]
}]
}
new_obj_info = self.ws.save_objects(ws_obj)
self.__class__.pairedEndLibInfo = new_obj_info[0]
return new_obj_info[0]