def construct_command(commandline_args):
"""Put together the command for the plugin"""
# The task to be carried out
command = {
"command": "ANALYSIS",
"process_id": uuid.uuid1().get_hex(),
}
# Working directory
if commandline_args.test:
# Don't make a new directory
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_analysis_%s" % ".".join(
os.path.basename(commandline_args.datafile).split(".")[:-1])),
active=False,
up=commandline_args.dir_up)
else:
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_analysis_%s" % ".".join(
os.path.basename(commandline_args.datafile).split(".")[:-1])),
active=True,
up=commandline_args.dir_up)
command["directories"] = {
"work": work_dir
}
# Information on input
command["input_data"] = {
"datafile": os.path.abspath(commandline_args.datafile),
"db_settings": commandline_args.db_settings,
}
# Plugin settings
command["preferences"] = {
"clean": commandline_args.clean,
#"dir_up": commandline_args.dir_up,
"nproc": commandline_args.nproc,
#"pdbquery": commandline_args.pdbquery,
"json": commandline_args.json,
"show_plots": commandline_args.show_plots,
"progress": commandline_args.progress,
"run_mode": commandline_args.run_mode,
"sample_type": commandline_args.sample_type,
"test": commandline_args.test,
#"computer_cluster": commandline_args.computer_cluster,
}
# Interprocess communication
#if commandline_args.queue:
# command["queue"] = commandline_args.queue
# logger.debug("Command for index plugin: %s", command)
return command
def construct_command(commandline_args):
"""Put together the command for the plugin"""
# The task to be carried out
command = {
"command": "ANALYSIS",
"process_id": uuid.uuid1().get_hex(),
}
# Working directory
if commandline_args.test:
# Don't make a new directory
work_dir = commandline_utils.check_work_dir(os.path.join(
os.path.abspath(os.path.curdir), "rapd_analysis_%s" % ".".join(
os.path.basename(commandline_args.data_file).split(".")[:-1])),
active=False,
up=commandline_args.dir_up)
else:
work_dir = commandline_utils.check_work_dir(os.path.join(
os.path.abspath(os.path.curdir), "rapd_analysis_%s" % ".".join(
os.path.basename(commandline_args.data_file).split(".")[:-1])),
active=True,
up=commandline_args.dir_up)
command["directories"] = {"work": work_dir}
# Information on input
command["input_data"] = {
"data_file": os.path.abspath(commandline_args.data_file),
"db_settings": commandline_args.db_settings,
}
# Plugin settings
command["preferences"] = {
"clean": commandline_args.clean,
#"dir_up": commandline_args.dir_up,
"nproc": commandline_args.nproc,
#"pdbquery": commandline_args.pdbquery,
"json": commandline_args.json,
"show_plots": commandline_args.show_plots,
"progress": commandline_args.progress,
"run_mode": commandline_args.run_mode,
"sample_type": commandline_args.sample_type,
"test": commandline_args.test,
#"computer_cluster": commandline_args.computer_cluster,
}
# Interprocess communication
#if commandline_args.queue:
# command["queue"] = commandline_args.queue
# logger.debug("Command for index plugin: %s", command)
return command
def construct_command(image_0_data, run_data, commandline_args, detector_module):
"""
Put together the command for the plugin
"""
# The task to be carried out
command = {
"command": "XDS", #"INTEGRATE",
"process": {"process_id": uuid.uuid1().get_hex()}
}
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_integrate_" + run_data["repr"]),
active=True,
up=commandline_args.dir_up)
# Where to do the work
command["directories"] = {
"work": work_dir
}
# Data data
command["data"] = {
"image_data": image_0_data,
"run_data": run_data
}
command["preferences"] = {
"analysis": commandline_args.analysis,
"pdbquery": commandline_args.pdbquery,
"clean_up": commandline_args.clean_up,
"computer_cluster": commandline_args.computer_cluster,
"dir_up": commandline_args.dir_up,
"exchange_dir": commandline_args.exchange_dir,
"start_frame": commandline_args.start_image,
"end_frame": commandline_args.end_image,
"flip_beam": detector_module.XDS_FLIP_BEAM,
"x_beam": commandline_args.beamcenter[0],
"y_beam": commandline_args.beamcenter[1],
"spacegroup": commandline_args.spacegroup,
"low_res": commandline_args.lowres,
"hi_res": commandline_args.hires,
"json": commandline_args.json,
"nproc": commandline_args.nproc,
"progress": commandline_args.progress,
"run_mode": commandline_args.run_mode,
"show_plots": commandline_args.show_plots,
"xdsinp": detector_module.XDSINP,
"spacegroup_decider": commandline_args.spacegroup_decider,
"rounds_polishing": commandline_args.rounds_polishing
}
if commandline_args.beamcenter[0]:
command["preferences"]["beam_center_override"] = True
return command
def construct_command(image_0_data, run_data, commandline_args, detector_module):
"""
Put together the command for the plugin
"""
# The task to be carried out
command = {
"command": "XDS", #"INTEGRATE",
"process": {"process_id": uuid.uuid1().get_hex()}
}
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_integrate_" + run_data["repr"]),
active=True,
up=commandline_args.dir_up)
# Where to do the work
command["directories"] = {
"work": work_dir
}
# Data data
command["data"] = {
"image_data": image_0_data,
"run_data": run_data
}
command["preferences"] = {
"analysis": commandline_args.analysis,
"pdbquery": commandline_args.pdbquery,
"clean_up": commandline_args.clean_up,
"computer_cluster": commandline_args.computer_cluster,
"dir_up": commandline_args.dir_up,
"exchange_dir": commandline_args.exchange_dir,
"start_frame": commandline_args.start_image,
"end_frame": commandline_args.end_image,
"flip_beam": detector_module.XDS_FLIP_BEAM,
"x_beam": commandline_args.beamcenter[0],
"y_beam": commandline_args.beamcenter[1],
"spacegroup": commandline_args.spacegroup,
"low_res": commandline_args.lowres,
"hi_res": commandline_args.hires,
"json": commandline_args.json,
"nproc": commandline_args.nproc,
"progress": commandline_args.progress,
"run_mode": commandline_args.run_mode,
"show_plots": commandline_args.show_plots,
"xdsinp": detector_module.XDSINP,
"spacegroup_decider": commandline_args.spacegroup_decider,
"rounds_polishing": commandline_args.rounds_polishing
}
if commandline_args.beamcenter[0]:
command["preferences"]["beam_center_override"] = True
return command
def construct_command(commandline_args):
"""
Put together the command for the plugin
commandline_args needs to look like:
class commandline_args(object):
clean = True | False
data_file = ""
struct_file = ""
json = True | False
no_color = True | False
nproc = int
progress = True | False
run_mode = "interactive" | "json" | "server" | "subprocess"
test = True | False
verbose = True | False
"""
# The task to be carried out
command = {
"command": "MR",
"process_id": uuid.uuid1().get_hex(),
"status": 0,
}
# Work directory
work_dir = commandline_utils.check_work_dir(os.path.join(
os.path.abspath(os.path.curdir), "rapd_mr_%s" % ".".join(
os.path.basename(commandline_args.data_file).split(".")[:-1])),
active=True,
up=commandline_args.dir_up)
command["directories"] = {
"work": work_dir,
"exchange_dir": commandline_args.exchange_dir
}
# Information on input
command["input_data"] = {
"data_file": os.path.abspath(commandline_args.data_file),
"struct_file": os.path.abspath(commandline_args.struct_file),
#"db_settings": commandline_args.db_settings
}
# Plugin settings
command["preferences"] = {
"clean": commandline_args.clean,
"json": commandline_args.json,
"nproc": commandline_args.nproc,
"progress": commandline_args.progress,
"run_mode": commandline_args.run_mode,
"test": commandline_args.test,
"adf": commandline_args.adf,
}
return command
def construct_command(commandline_args, logger):
"""
Put together the command for the plugin
commandline_args needs to look like:
class commandline_args(object):
clean = True | False
datafile = ""
json = True | False
no_color = True | False
nproc = int
progress = True | False
run_mode = "interactive" | "json" | "server" | "subprocess"
test = True | False
verbose = True | False
"""
# The task to be carried out
command = {
"command": "HCMERGE",
"process_id": uuid.uuid1().get_hex(),
"status": 0,
}
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"hcmerge"),
active=True,
up=commandline_args.dir_up)
# Work directory
command["directories"] = {
"work": work_dir
}
# Information on input
command["input_data"] = {
"datasets": commandline_args.datasets
}
# Plugin settings
command["preferences"] = {
"json": commandline_args.json,
"nproc": commandline_args.nproc,
"run_mode": commandline_args.run_mode,
"test": commandline_args.test,
}
for setting in commandline_args._get_kwargs():
command['preferences'][setting[0]] = setting[1]
logger.debug("Command for hcmerge plugin: %s", command)
return command
def construct_command(commandline_args):
"""Put together the command for the plugin"""
# The task to be carried out
command = {
"command": "ECHO",
"process_id": uuid.uuid1().get_hex(),
"status": 0,
}
# Work directory
work_dir = commandline_utils.check_work_dir(
os.path.join(os.path.abspath(os.path.curdir), run_repr),
active=True,
up=commandline_args.dir_up)
command["directories"] = {
"work": work_dir
}
# Check the work directory
commandline_utils.check_work_dir(command["directories"]["work"], True)
# Information on input
command["input_data"] = {
"datafile": os.path.abspath(commandline_args.datafile)
}
# Plugin settings
command["preferences"] = {
"clean": commandline_args.clean,
"json": commandline_args.json,
"no_color": commandline_args.no_color,
"nproc": commandline_args.nproc,
"progress": commandline_args.progress,
"test": commandline_args.test,
"verbose": commandline_args.verbose,
}
return command
def construct_command(commandline_args):
"""Put together the command for the plugin"""
# The task to be carried out
command = {
"command": "ECHO",
"process_id": uuid.uuid1().get_hex(),
"status": 0,
}
# Work directory
work_dir = commandline_utils.check_work_dir(os.path.join(
os.path.abspath(os.path.curdir), run_repr),
active=True,
up=commandline_args.dir_up)
command["directories"] = {"work": work_dir}
# Check the work directory
commandline_utils.check_work_dir(command["directories"]["work"], True)
# Information on input
command["input_data"] = {
"datafile": os.path.abspath(commandline_args.datafile)
}
# Plugin settings
command["preferences"] = {
"clean": commandline_args.clean,
"json": commandline_args.json,
"no_color": commandline_args.no_color,
"nproc": commandline_args.nproc,
"progress": commandline_args.progress,
"test": commandline_args.test,
"verbose": commandline_args.verbose,
}
return command
def construct_command(commandline_args, logger):
"""
Put together the command for the plugin
commandline_args needs to look like:
class commandline_args(object):
clean = True | False
datafile = ""
json = True | False
no_color = True | False
nproc = int
progress = True | False
run_mode = "interactive" | "json" | "server" | "subprocess"
test = True | False
verbose = True | False
"""
# The task to be carried out
command = {
"command": "HCMERGE",
"process_id": uuid.uuid1().get_hex(),
"status": 0,
}
work_dir = commandline_utils.check_work_dir(os.path.join(
os.path.abspath(os.path.curdir), "hcmerge"),
active=True,
up=commandline_args.dir_up)
# Work directory
command["directories"] = {"work": work_dir}
# Information on input
command["input_data"] = {"datasets": commandline_args.datasets}
# Plugin settings
command["preferences"] = {
"json": commandline_args.json,
"nproc": commandline_args.nproc,
"run_mode": commandline_args.run_mode,
"test": commandline_args.test,
}
for setting in commandline_args._get_kwargs():
command['preferences'][setting[0]] = setting[1]
logger.debug("Command for hcmerge plugin: %s", command)
return command
def construct_command(commandline_args):
"""
Put together the command for the plugin
commandline_args needs to look like:
class commandline_args(object):
clean = True | False
contaminants = True | False
datafile = ""
json = True | False
no_color = True | False
nproc = int
pdbs = False | ["pdbid", ...]
progress = True | False
run_mode = "interactive" | "json" | "server" | "subprocess"
search = True | False
test = True | False
verbose = True | False
"""
# The task to be carried out
command = {
"command": "PDBQUERY",
"process_id": uuid.uuid1().get_hex(),
"status": 0,
}
# Work directory
"""
if commandline_args.test:
# Don't make a new directory
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_pdbquery_%s" % ".".join(
os.path.basename(commandline_args.datafile).split(".")[:-1])),
active=False,
up=commandline_args.dir_up)
else:
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_pdbquery_%s" % ".".join(
os.path.basename(commandline_args.datafile).split(".")[:-1])),
active=True,
up=commandline_args.dir_up)
"""
work_dir = commandline_utils.check_work_dir(
os.path.join(
os.path.abspath(os.path.curdir),
"rapd_pdbquery_%s" % ".".join(
os.path.basename(commandline_args.datafile).split(".")[:-1])),
active=True,
up=commandline_args.dir_up)
command["directories"] = {
"work": work_dir,
"exchange_dir": commandline_args.exchange_dir
}
# Information on input
command["input_data"] = {
"datafile": os.path.abspath(commandline_args.datafile),
"pdbs": commandline_args.pdbs,
"db_settings": commandline_args.db_settings
}
# Plugin settings
command["preferences"] = {
"clean": commandline_args.clean,
"json": commandline_args.json,
"contaminants": commandline_args.contaminants,
"nproc": commandline_args.nproc,
"progress": commandline_args.progress,
"run_mode": commandline_args.run_mode,
"search": commandline_args.search,
"test": commandline_args.test,
#"computer_cluster": commandline_args.computer_cluster,
#"results_queue": commandline_args.results_queue,
}
return command
def construct_command(image_headers, commandline_args, detector_module):
"""
Put together the command for the plugin
"""
# The task to be carried out
command = {
"command": "INDEX",
"process": {
"process_id": uuid.uuid1().get_hex(),
"parent_id": None,
"source": "commandline",
"status": 0
}
}
# Working directory
image_numbers = []
image_template = ""
h5 = ""
for _, header in image_headers.iteritems():
image_numbers.append(str(header["image_number"]))
image_template = header["image_template"]
if "hdf5_source" in header:
if h5:
h5 += "_"
h5 += os.path.basename(header["hdf5_source"]).replace("_master.h5", "")
image_numbers.sort()
if h5:
run_repr = "rapd_index_" + h5
else:
run_repr = "rapd_index_" + image_template.replace(detector_module.DETECTOR_SUFFIX, "").\
replace("?", "")
run_repr += "+".join(image_numbers)
work_dir = commandline_utils.check_work_dir(
os.path.join(os.path.abspath(os.path.curdir), run_repr),
active=True,
up=commandline_args.dir_up)
command["directories"] = {
"work": work_dir
}
# Image data
images = image_headers.keys()
images.sort()
counter = 0
for image in images:
counter += 1
command["image%d" % counter] = image_headers[image]
if counter == 1:
command["image2"] = None
# Plugin settings
command["preferences"] = {}
# JSON output?
command["preferences"]["json"] = commandline_args.json
command["preferences"]["json_fd"] = commandline_args.json_fd
command["preferences"]["progress"] = commandline_args.progress
command["preferences"]["no_color"] = commandline_args.no_color
# Show plots
command["preferences"]["show_plots"] = commandline_args.show_plots
# Strategy type
command["preferences"]["strategy_type"] = commandline_args.strategy_type
# Best
command["preferences"]["best_complexity"] = commandline_args.best_complexity
command["preferences"]["shape"] = 2.0
command["preferences"]["susceptibility"] = 1.0
command["preferences"]["aimed_res"] = 0.0
# Best & Labelit
command["preferences"]["sample_type"] = commandline_args.sample_type
command["preferences"]["spacegroup"] = commandline_args.spacegroup
command["preferences"]["unitcell"] = commandline_args.unitcell
# Labelit
command["preferences"]["index_hi_res"] = try_float(commandline_args.hires, 0.0)
command["preferences"]["x_beam"] = commandline_args.beamcenter[0]
command["preferences"]["y_beam"] = commandline_args.beamcenter[1]
command["preferences"]["beam_search"] = commandline_args.beam_search
# Mosflm
command["preferences"]["mosflm_rot"] = float(commandline_args.mosflm_range)
command["preferences"]["mosflm_seg"] = int(commandline_args.mosflm_segments)
command["preferences"]["mosflm_start"] = float(commandline_args.mosflm_start)
command["preferences"]["mosflm_end"] = float(commandline_args.mosflm_end)
command["preferences"]["reference_data"] = None
command["preferences"]["reference_data_id"] = None
# Change these if user wants to continue dataset with other crystal(s).
# "reference_data_id": None, #MOSFLM
# #"reference_data_id": 1,#MOSFLM
# #"reference_data": [['/gpfs6/users/necat/Jon/RAPD_test/index09.mat', 0.0, 30.0, 'junk_1_1-30',
# 'P41212']],#MOSFLM
# 'reference_data': [['/gpfs6/users/necat/Jon/RAPD_test/Output/junk/5/index12.mat',
# 0.0,
# 20.0,
# 'junk',
# 'P3'],
# ['/gpfs6/users/necat/Jon/RAPD_test/Output/junk/5/index12.mat',
# 40.0,
# 50.0,
# 'junk2',
# 'P3']
# ],#MOSFLM
# Raddose
command["preferences"]["crystal_size_x"] = 100.0
command["preferences"]["crystal_size_y"] = 100.0
command["preferences"]["crystal_size_z"] = 100.0
command["preferences"]["solvent_content"] = commandline_args.solvent
#command["preferences"][]
# Unknown
command["preferences"]["beam_flip"] = False
#command["preferences"]["multiprocessing"] = False
# Launches jobs at same time using more cores. Much Faster!!
#command["preferences"]["multiprocessing"] = True
command["preferences"]["nproc"] = commandline_args.nproc
# The run mode for rapd
command["preferences"]["run_mode"] = commandline_args.run_mode
# Site parameters
command["preferences"]["site_parameters"] = {}
command["preferences"]["site_parameters"]["DETECTOR_DISTANCE_MAX"] = \
commandline_args.site_det_dist_max
command["preferences"]["site_parameters"]["DETECTOR_DISTANCE_MIN"] = \
commandline_args.site_det_dist_min
command["preferences"]["site_parameters"]["DIFFRACTOMETER_OSC_MIN"] = \
commandline_args.site_osc_min
command["preferences"]["site_parameters"]["DETECTOR_TIME_MIN"] = \
commandline_args.site_det_time_min
return command
def construct_command(image_headers, commandline_args, detector_module):
"""
Put together the command for the plugin
"""
# The task to be carried out
command = {
"command": "INDEX",
"process": {
"process_id": uuid.uuid1().get_hex(),
"parent_id": None,
"source": "commandline",
"status": 0
}
}
# Working directory
image_numbers = []
image_template = ""
h5 = ""
for _, header in image_headers.iteritems():
image_numbers.append(str(header["image_number"]))
image_template = header["image_template"]
if "hdf5_source" in header:
if h5:
h5 += "_"
h5 += os.path.basename(header["hdf5_source"]).replace("_master.h5", "")
image_numbers.sort()
if h5:
run_repr = "rapd_index_" + h5
else:
run_repr = "rapd_index_" + image_template.replace(detector_module.DETECTOR_SUFFIX, "").\
replace("?", "")
run_repr += "+".join(image_numbers)
work_dir = commandline_utils.check_work_dir(
os.path.join(os.path.abspath(os.path.curdir), run_repr),
active=True,
up=commandline_args.dir_up)
command["directories"] = {
"work": work_dir
}
# Image data
images = image_headers.keys()
images.sort()
counter = 0
for image in images:
counter += 1
command["image%d" % counter] = image_headers[image]
if counter == 1:
command["image2"] = None
# Plugin settings
command["preferences"] = {}
# JSON output?
command["preferences"]["json"] = commandline_args.json
command["preferences"]["json_fd"] = commandline_args.json_fd
command["preferences"]["progress"] = commandline_args.progress
command["preferences"]["no_color"] = commandline_args.no_color
# Show plots
command["preferences"]["show_plots"] = commandline_args.show_plots
# Strategy type
command["preferences"]["strategy_type"] = commandline_args.strategy_type
# Best
command["preferences"]["best_complexity"] = commandline_args.best_complexity
command["preferences"]["shape"] = 2.0
command["preferences"]["susceptibility"] = 1.0
command["preferences"]["aimed_res"] = 0.0
command["preferences"]["aimed_redundancy"] = commandline_args.best_aimed_redundancy
# Best & Labelit
command["preferences"]["sample_type"] = commandline_args.sample_type
command["preferences"]["spacegroup"] = commandline_args.spacegroup
command["preferences"]["unitcell"] = commandline_args.unitcell
# Labelit
command["preferences"]["index_hi_res"] = try_float(commandline_args.hires, 0.0)
command["preferences"]["x_beam"] = commandline_args.beamcenter[0]
command["preferences"]["y_beam"] = commandline_args.beamcenter[1]
command["preferences"]["beam_search"] = commandline_args.beam_search
# Mosflm
command["preferences"]["mosflm_rot"] = float(commandline_args.mosflm_range)
command["preferences"]["mosflm_seg"] = int(commandline_args.mosflm_segments)
command["preferences"]["mosflm_start"] = float(commandline_args.mosflm_start)
command["preferences"]["mosflm_end"] = float(commandline_args.mosflm_end)
command["preferences"]["reference_data"] = None
command["preferences"]["reference_data_id"] = None
# Change these if user wants to continue dataset with other crystal(s).
# "reference_data_id": None, #MOSFLM
# #"reference_data_id": 1,#MOSFLM
# #"reference_data": [['/gpfs6/users/necat/Jon/RAPD_test/index09.mat', 0.0, 30.0, 'junk_1_1-30',
# 'P41212']],#MOSFLM
# 'reference_data': [['/gpfs6/users/necat/Jon/RAPD_test/Output/junk/5/index12.mat',
# 0.0,
# 20.0,
# 'junk',
# 'P3'],
# ['/gpfs6/users/necat/Jon/RAPD_test/Output/junk/5/index12.mat',
# 40.0,
# 50.0,
# 'junk2',
# 'P3']
# ],#MOSFLM
# Raddose
command["preferences"]["crystal_size_x"] = 100.0
command["preferences"]["crystal_size_y"] = 100.0
command["preferences"]["crystal_size_z"] = 100.0
command["preferences"]["solvent_content"] = commandline_args.solvent
#command["preferences"][]
# Unknown
command["preferences"]["beam_flip"] = False
#command["preferences"]["multiprocessing"] = False
# Launches jobs at same time using more cores. Much Faster!!
#command["preferences"]["multiprocessing"] = True
command["preferences"]["nproc"] = commandline_args.nproc
# The run mode for rapd
command["preferences"]["run_mode"] = commandline_args.run_mode
# Site parameters
command["preferences"]["site_parameters"] = {}
command["preferences"]["site_parameters"]["DETECTOR_DISTANCE_MAX"] = \
commandline_args.site_det_dist_max
command["preferences"]["site_parameters"]["DETECTOR_DISTANCE_MIN"] = \
commandline_args.site_det_dist_min
command["preferences"]["site_parameters"]["DIFFRACTOMETER_OSC_MIN"] = \
commandline_args.site_osc_min
command["preferences"]["site_parameters"]["DETECTOR_TIME_MIN"] = \
commandline_args.site_det_time_min
return command