def delete_data(file_id, collection_id=None):
if in_orion():
if collection_id is None:
raise ValueError("The Collection ID is None")
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = session.get_resource(ShardCollection, collection_id)
session.delete_resource(Shard(collection=collection, id=file_id))
else:
os.remove(file_id)
return True
def upload_data(filename, collection_id=None, shard_name=""):
if in_orion():
if collection_id is None:
raise ValueError("The Collection ID is None")
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = session.get_resource(ShardCollection, collection_id)
shard = try_hard_to_create_shard(collection, filename, name=shard_name)
file_id = shard.id
shard.close()
else:
file_id = filename
return file_id
def delete_file(file_id):
if in_orion():
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
resource = session.get_resource(File, file_id)
session.delete_resource(resource)
else:
os.remove(file_id)
return True
def download_file(file_id, filename):
if in_orion():
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
resource = session.get_resource(File, file_id)
resource.download_to_file(filename)
fn_local = filename
else:
fn_local = file_id
if not os.path.isfile(fn_local):
raise IOError(
"The trajectory file has not been found: {}".format(fn_local))
return fn_local
def upload_file(filename, orion_ui_name='OrionFile'):
if in_orion():
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
file_upload = File.upload(session, orion_ui_name, filename)
session.tag_resource(file_upload, "Trajectory")
job_id = environ.get('ORION_JOB_ID')
if job_id:
session.tag_resource(file_upload, "Job {}".format(job_id))
file_id = file_upload.id
else:
file_id = filename
return file_id
def get_protein_traj(self):
"""
This method returns the protein molecule where conformers have been set as trajectory frames
Parameters
----------
Returns
-------
multi_conformer_protein: OEMol
The multi conformer protein
"""
if not self.rec.has_field(Fields.protein_traj_confs):
raise ValueError(
"The protein conformer trajectory is not present on the record"
)
protein_conf = self.rec.get_value(Fields.protein_traj_confs)
if in_orion():
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
if self.collection_id is None:
raise ValueError("The Collection ID is None")
collection = session.get_resource(ShardCollection,
self.collection_id)
shard = session.get_resource(Shard(collection=collection),
protein_conf)
with TemporaryDirectory() as output_directory:
protein_fn = os.path.join(output_directory,
MDFileNames.trajectory_conformers)
try_hard_to_download_shard(shard, protein_fn)
protein_conf = oechem.OEMol()
with oechem.oemolistream(protein_fn) as ifs:
oechem.OEReadMolecule(ifs, protein_conf)
shard.close()
return protein_conf
def main(ctx, profile):
ctx.obj = dict()
ctx.obj['session'] = orionclient.session.OrionSession(
orionclient.session.get_profile_config(profile=profile),
requests_session=get_session(retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
def create_collection(self, name):
"""
This method sets a collection field on the record to be used in Orion
Parameters
-----------
name: String
A string used to identify in the Orion UI the collection
Returns
-------
boolean : Bool
True if the collection creation in Orion was successful otherwise False
"""
if in_orion():
if self.rec.has_field(Fields.collection):
raise ValueError(
"Collection field already present on the record")
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = ShardCollection.create(session, name)
self.rec.set_value(Fields.collection, collection.id)
self.collection_id = collection.id
else:
return False
return True
def delete_parmed(self):
"""
This method deletes the Parmed object from the record. True is returned if the deletion was
successful.
Parameters
----------
Returns
-------
boolean : Bool
True if Parmed object deletion was successful
"""
if not self.has_parmed:
raise ValueError(
"The Parmed structure is not present on the record")
if in_orion():
if self.collection_id is None:
raise ValueError("The Collection ID is None")
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = session.get_resource(ShardCollection,
self.collection_id)
file_id = self.rec.get_value(Fields.pmd_structure)
session.delete_resource(Shard(collection=collection, id=file_id))
self.rec.delete_field(Fields.pmd_structure)
return True
def download_data(file_id, path, collection_id=None):
if in_orion():
if collection_id is None:
raise ValueError("The Collection ID is None")
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = session.get_resource(ShardCollection, collection_id)
shard = session.get_resource(Shard(collection=collection), file_id)
from MDOrion.Standards import MDFileNames
fn_local = os.path.join(path, MDFileNames.mddata)
try_hard_to_download_shard(shard, fn_local)
shard.close()
else:
fn_local = file_id
if not os.path.isfile(fn_local):
raise IOError(
"The MD data file has not been found: {}".format(fn_local))
return fn_local
def set_protein_traj(self, protein_conf, shard_name=""):
"""
This method sets the multi conformer protein trajectory on the record
Parameters
-----------
protein_conf: OEChem
Th multi conformer protein trajectory
shard_name: String
In Orion tha shard will be named by using the shard_name
Returns
-------
boolean: Bool
True if the setting was successful
"""
if not isinstance(protein_conf, oechem.OEMol):
raise ValueError(
"The passed Parmed object is not a valid Parmed Structure: {}".
format(type(protein_conf)))
if in_orion():
with TemporaryDirectory() as output_directory:
protein_fn = os.path.join(output_directory,
MDFileNames.trajectory_conformers)
with oechem.oemolostream(protein_fn) as ofs:
oechem.OEWriteConstMolecule(ofs, protein_conf)
if self.collection_id is None:
raise ValueError("The Collection ID is None")
if self.rec.has_field(Fields.protein_traj_confs):
fid = self.rec.get_value(Fields.protein_traj_confs)
utils.delete_data(fid, collection_id=self.collection_id)
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = session.get_resource(ShardCollection,
self.collection_id)
shard = try_hard_to_create_shard(collection,
protein_fn,
name=shard_name)
shard.close()
self.rec.set_value(Fields.protein_traj_confs, shard.id)
else:
self.rec.set_value(Fields.protein_traj_confs, protein_conf)
return True
def set_parmed(self, pmd, sync_stage_name=None, shard_name=""):
"""
This method sets the Parmed object. Return True if the setting was successful.
If sync_stage_name is not None the parmed structure positions, velocities and
box vectors will be synchronized with the MD State selected by passing the MD
stage name
Parameters
----------
pmd: Parmed Structure object
The Parmed Structure object to be set on the record
sync_stage_name: String or None
The stage name that is used to synchronize the Parmed structure
shard_name: String
In Orion tha shard will be named by using the shard_name
Returns
-------
boolean : Bool
True if the setting was successful
"""
if not isinstance(pmd, parmed.Structure):
raise ValueError(
"The passed Parmed object is not a valid Parmed Structure: {}".
format(type(pmd)))
if sync_stage_name is not None:
mdstate = self.get_stage_state(stg_name=sync_stage_name)
pmd.positions = mdstate.get_positions()
pmd.velocities = mdstate.get_velocities()
pmd.box_vectors = mdstate.get_box_vectors()
if in_orion():
with TemporaryDirectory() as output_directory:
parmed_fn = os.path.join(output_directory, 'parmed.pickle')
with open(parmed_fn, 'wb') as f:
pickle.dump(pmd.__getstate__(), f)
if self.collection_id is None:
raise ValueError("The Collection ID is None")
if self.rec.has_field(Fields.pmd_structure):
fid = self.rec.get_value(Fields.pmd_structure)
utils.delete_data(fid, collection_id=self.collection_id)
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
collection = session.get_resource(ShardCollection,
self.collection_id)
shard = try_hard_to_create_shard(collection,
parmed_fn,
name=shard_name)
shard.close()
self.rec.set_value(Fields.pmd_structure, shard.id)
else:
self.rec.set_value(Fields.pmd_structure, pmd)
return True
def get_parmed(self, sync_stage_name=None):
"""
This method returns the Parmed object. An exception is raised if the Parmed object cannot
be found. If sync_stage_name is not None the parmed structure positions, velocities and
box vectors will be synchronized with the MD State selected by passing the MD stage name
Parameters
----------
sync_stage_name: String or None
The stage name that is used to synchronize the Parmed structure
Returns
-------
parmed : Parmed Structure
The Parmed Structure object
"""
if not self.rec.has_field(Fields.pmd_structure):
raise ValueError(
"The Parmed reference is not present on the record")
pmd_structure = self.rec.get_value(Fields.pmd_structure)
if in_orion():
# session = APISession
session = OrionSession(requests_session=get_session(
retry_dict={
403: 5,
404: 20,
409: 45,
460: 15,
500: 2,
502: 45,
503: 45,
504: 45,
}))
if self.collection_id is None:
raise ValueError("The Collection ID is None")
collection = session.get_resource(ShardCollection,
self.collection_id)
shard = session.get_resource(Shard(collection=collection),
pmd_structure)
with TemporaryDirectory() as output_directory:
parmed_fn = os.path.join(output_directory, "parmed.pickle")
try_hard_to_download_shard(shard, parmed_fn)
with open(parmed_fn, 'rb') as f:
parm_dic = pickle.load(f)
pmd_structure = parmed.structure.Structure()
pmd_structure.__setstate__(parm_dic)
shard.close()
if sync_stage_name is not None:
mdstate = self.get_stage_state(stg_name=sync_stage_name)
pmd_structure.positions = mdstate.get_positions()
pmd_structure.velocities = mdstate.get_velocities()
pmd_structure.box_vectors = mdstate.get_box_vectors()
return pmd_structure