def get_employee(self, employee_id, field_list=None):
"""
API method for returning a single employee based on employee id.
http://www.bamboohr.com/api/documentation/employees.php#getEmployee
@param employee_id: String of the employee id.
@param field_list: List of fields to return with the employee dictionary.
@return: A dictionary containing employee information from the specified field list.
"""
get_fields = []
field_list = [utils.underscore_to_camelcase(field) for field in field_list] if field_list else None
if field_list:
for f in field_list:
get_fields.append(f)
else:
for field in self.employee_fields:
get_fields.append(field)
payload = {
'fields': ",".join(get_fields)
}
url = self.base_url + "employees/{0}".format(employee_id)
r = requests.get(url, headers=self.headers, params=payload, auth=(self.api_key, 'x'))
r.raise_for_status()
employee = r.json()
if self.underscore_keys:
employee = utils.underscore_keys(employee)
return employee
def request_custom_report(self, field_list, report_format='xls', title="My Custom Report", output_filename=None):
"""
API method for returning a custom report by field list.
http://www.bamboohr.com/api/documentation/employees.php#requestCustomReport
Success Response: 200
The report will be generated in the requested format.
The HTTP Content-type header will be set with the mime type for the response.
@param fields: List of report fields
@param report_format: String of the format to receive the report. (csv, pdf, xls, xml)
@param output_filename: String (optional) if a filename/location is passed, the results will be saved to disk
@return: A result in the format specified. (Will vary depending on format requested.)
"""
report_formats = self.report_formats
report_formats.pop('json')
if report_format not in report_formats:
raise UserWarning("You requested an invalid report type. Valid values are: {0}".format(','.join([k for k in report_formats])))
get_fields = []
field_list = [underscore_to_camelcase(field) for field in field_list] if field_list else None
if field_list:
for f in field_list:
if not self.employee_fields.get(f):
raise UserWarning("You passed in an invalid field")
else:
get_fields.append(f)
else:
for field in self.employee_fields:
get_fields.append(field)
xml = self._format_report_xml(get_fields, title=title, report_format=report_format)
url = self.base_url + "reports/custom/?format={0}".format(report_format)
r = requests.post(url, data=xml, headers=self.headers, auth=(self.api_key, ''))
r.raise_for_status()
if report_format == 'json':
# return list/dict for json type
result = r.json()
elif report_format in ('csv', 'xml'):
# return text for csv type
result = r.text
else:
# return requests object for everything else after saving the file to the location specified.
result = r
if output_filename:
with open(output_filename, 'wb') as handle:
for block in r.iter_content(1024):
if not block:
break
handle.write(block)
return result
def _parserBodyCommand(self, body, delimiter='|'):
output = {}
if body:
tmp = body.splitlines()
if len(tmp) > 0:
header = tmp[0].split(delimiter)
for l in tmp[1:-1]:
line = l.split(delimiter)
if len(line) < len(header):
continue
i = 0
tmp_dict = {}
for e in line:
tmp_dict[utils.underscore_to_camelcase(header[i])] = e
i = i + 1
output[line[0]] = tmp_dict
return output
def _parserBodyCommand(self, body, delimiter='|'):
output = {}
if body:
tmp = body.splitlines()
if len(tmp) > 0:
header = tmp[0].split(delimiter)
for l in tmp[1:-1]:
line = l.split(delimiter)
if len(line) < len(header):
continue
i = 0
tmp_dict = {}
for e in line:
tmp_dict[utils.underscore_to_camelcase(header[i])] = e
i = i + 1
output[line[0]] = tmp_dict
return output
def prepare_phase(positions_file_path,
topology_file_path,
ligand_dsl,
system_options,
gromacs_include_dir=None,
verbose=False):
"""Create a Yank arguments for a phase from system files.
Parameters
----------
positions_file_path : str
Path to system position file (e.g. 'complex.inpcrd' or 'complex.gro').
topology_file_path : str
Path to system topology file (e.g. 'complex.prmtop' or 'complex.top').
ligand_dsl : str
MDTraj DSL string that specify the ligand atoms.
system_options : dict
system_options[phase] is a a dictionary containing options to pass to createSystem().
gromacs_include_dir : str, optional
Path to directory in which to look for other files included from the gromacs top file.
verbose : bool
Whether or not to log information (default is False).
Returns
-------
alchemical_phase : AlchemicalPhase
The alchemical phase for Yank calculation with unspecified name, and protocol.
"""
# Load system files
if os.path.splitext(topology_file_path)[1] == '.prmtop':
# Read Amber prmtop and inpcrd files
if verbose:
logger.info("prmtop: %s" % topology_file_path)
logger.info("inpcrd: %s" % positions_file_path)
topology_file = openmm.app.AmberPrmtopFile(topology_file_path)
positions_file = openmm.app.AmberInpcrdFile(positions_file_path)
box_vectors = positions_file.boxVectors
create_system_args = set(
inspect.getargspec(openmm.app.AmberPrmtopFile.createSystem).args)
else:
# Read Gromacs top and gro files
if verbose:
logger.info("top: %s" % topology_file_path)
logger.info("gro: %s" % positions_file_path)
positions_file = openmm.app.GromacsGroFile(positions_file_path)
box_vectors = positions_file.getPeriodicBoxVectors()
topology_file = openmm.app.GromacsTopFile(
topology_file_path,
periodicBoxVectors=box_vectors,
includeDir=gromacs_include_dir)
create_system_args = set(
inspect.getargspec(openmm.app.GromacsTopFile.createSystem).args)
# Prepare createSystem() options
# OpenMM adopts camel case convention so we need to change the options format.
# Then we filter system options according to specific createSystem() args
system_options = {
utils.underscore_to_camelcase(key): value
for key, value in system_options.items()
}
system_options = {
arg: system_options[arg]
for arg in create_system_args if arg in system_options
}
# Determine if this will be an explicit or implicit solvent simulation.
if box_vectors is not None:
is_periodic = True
else:
is_periodic = False
# Adjust nonbondedMethod
# TODO: Ensure that selected method is appropriate.
if 'nonbondedMethod' not in system_options:
if is_periodic:
system_options['nonbondedMethod'] = openmm.app.CutoffPeriodic
else:
system_options['nonbondedMethod'] = openmm.app.NoCutoff
# Check for solvent configuration inconsistencies
# TODO: Check to make sure both files agree on explicit/implicit.
err_msg = ''
if is_periodic:
if 'implicitSolvent' in system_options:
err_msg = 'Found periodic box in inpcrd file and implicitSolvent specified.'
if system_options['nonbondedMethod'] == openmm.app.NoCutoff:
err_msg = 'Found periodic box in inpcrd file but nonbondedMethod is NoCutoff'
else:
if system_options['nonbondedMethod'] != openmm.app.NoCutoff:
err_msg = 'nonbondedMethod is NoCutoff but could not find periodic box in inpcrd.'
if len(err_msg) != 0:
logger.error(err_msg)
raise RuntimeError(err_msg)
# Create system and update box vectors (if needed)
system = topology_file.createSystem(removeCMMotion=False, **system_options)
if is_periodic:
system.setDefaultPeriodicBoxVectors(*box_vectors)
# Store numpy positions
positions = positions_file.getPositions(asNumpy=True)
# Check to make sure number of atoms match between prmtop and inpcrd.
topology_natoms = system.getNumParticles()
positions_natoms = positions.shape[0]
if topology_natoms != positions_natoms:
err_msg = "Atom number mismatch: {} has {} atoms; {} has {} atoms.".format(
topology_file_path, topology_natoms, positions_file_path,
positions_natoms)
logger.error(err_msg)
raise RuntimeError(err_msg)
# Find ligand atoms and receptor atoms
atom_indices = find_components(system, topology_file.topology, ligand_dsl)
alchemical_phase = AlchemicalPhase('', system, topology_file.topology,
positions, atom_indices, None)
return alchemical_phase
def prepare_phase(positions_file_path, topology_file_path, ligand_dsl, system_options,
gromacs_include_dir=None, verbose=False):
"""Create a Yank arguments for a phase from system files.
Parameters
----------
positions_file_path : str
Path to system position file (e.g. 'complex.inpcrd' or 'complex.gro').
topology_file_path : str
Path to system topology file (e.g. 'complex.prmtop' or 'complex.top').
ligand_dsl : str
MDTraj DSL string that specify the ligand atoms.
system_options : dict
system_options[phase] is a a dictionary containing options to pass to createSystem().
gromacs_include_dir : str, optional
Path to directory in which to look for other files included from the gromacs top file.
verbose : bool
Whether or not to log information (default is False).
Returns
-------
alchemical_phase : AlchemicalPhase
The alchemical phase for Yank calculation with unspecified name, and protocol.
"""
# Load system files
if os.path.splitext(topology_file_path)[1] == '.prmtop':
# Read Amber prmtop and inpcrd files
if verbose:
logger.info("prmtop: %s" % topology_file_path)
logger.info("inpcrd: %s" % positions_file_path)
topology_file = openmm.app.AmberPrmtopFile(topology_file_path)
positions_file = openmm.app.AmberInpcrdFile(positions_file_path)
box_vectors = positions_file.boxVectors
create_system_args = set(inspect.getargspec(openmm.app.AmberPrmtopFile.createSystem).args)
else:
# Read Gromacs top and gro files
if verbose:
logger.info("top: %s" % topology_file_path)
logger.info("gro: %s" % positions_file_path)
positions_file = openmm.app.GromacsGroFile(positions_file_path)
box_vectors = positions_file.getPeriodicBoxVectors()
topology_file = openmm.app.GromacsTopFile(topology_file_path,
periodicBoxVectors=box_vectors,
includeDir=gromacs_include_dir)
create_system_args = set(inspect.getargspec(openmm.app.GromacsTopFile.createSystem).args)
# Prepare createSystem() options
# OpenMM adopts camel case convention so we need to change the options format.
# Then we filter system options according to specific createSystem() args
system_options = {utils.underscore_to_camelcase(key): value
for key, value in system_options.items()}
system_options = {arg: system_options[arg] for arg in create_system_args
if arg in system_options}
# Determine if this will be an explicit or implicit solvent simulation.
if box_vectors is not None:
is_periodic = True
else:
is_periodic = False
# Adjust nonbondedMethod
# TODO: Ensure that selected method is appropriate.
if 'nonbondedMethod' not in system_options:
if is_periodic:
system_options['nonbondedMethod'] = openmm.app.CutoffPeriodic
else:
system_options['nonbondedMethod'] = openmm.app.NoCutoff
# Check for solvent configuration inconsistencies
# TODO: Check to make sure both files agree on explicit/implicit.
err_msg = ''
if is_periodic:
if 'implicitSolvent' in system_options:
err_msg = 'Found periodic box in inpcrd file and implicitSolvent specified.'
if system_options['nonbondedMethod'] == openmm.app.NoCutoff:
err_msg = 'Found periodic box in inpcrd file but nonbondedMethod is NoCutoff'
else:
if system_options['nonbondedMethod'] != openmm.app.NoCutoff:
err_msg = 'nonbondedMethod is NoCutoff but could not find periodic box in inpcrd.'
if len(err_msg) != 0:
logger.error(err_msg)
raise RuntimeError(err_msg)
# Create system and update box vectors (if needed)
system = topology_file.createSystem(removeCMMotion=False, **system_options)
if is_periodic:
system.setDefaultPeriodicBoxVectors(*box_vectors)
# Store numpy positions
positions = positions_file.getPositions(asNumpy=True)
# Check to make sure number of atoms match between prmtop and inpcrd.
topology_natoms = system.getNumParticles()
positions_natoms = positions.shape[0]
if topology_natoms != positions_natoms:
err_msg = "Atom number mismatch: {} has {} atoms; {} has {} atoms.".format(
topology_file_path, topology_natoms, positions_file_path, positions_natoms)
logger.error(err_msg)
raise RuntimeError(err_msg)
# Find ligand atoms and receptor atoms
atom_indices = find_components(system, topology_file.topology, ligand_dsl)
alchemical_phase = AlchemicalPhase('', system, topology_file.topology,
positions, atom_indices, None)
return alchemical_phase