def create_autoproc_input(self, event, params):
"""Creates processing input xml
:param event: processing type (after, before, image)
:type event: str
:param params: collection parameters
:type params: dict
"""
xds_input_file_wait_timeout = 20
xds_input_file_wait_resolution = 1
file_name_timestamp = time.strftime("%Y%m%d_%H%M%S")
autoproc_path = params.get("xds_dir")
autoproc_xds_filename = os.path.join(autoproc_path, "XDS.INP")
autoproc_input_filename = os.path.join(\
autoproc_path,
"edna-autoproc-input-%s.xml" % \
file_name_timestamp)
autoproc_output_file_name = os.path.join(\
autoproc_path,
"edna-autoproc-results-%s.xml" % \
file_name_timestamp)
autoproc_input = XSDataAutoprocInput()
autoproc_xds_file = XSDataFile()
autoproc_xds_file.setPath(XSDataString(autoproc_xds_filename))
autoproc_input.setInput_file(autoproc_xds_file)
autoproc_output_file = XSDataFile()
autoproc_output_file.setPath(XSDataString(autoproc_output_file_name))
autoproc_input.setOutput_file(autoproc_output_file)
autoproc_input.setData_collection_id(\
XSDataInteger(params.get("collection_id")))
residues_num = float(params.get("residues", 0))
if residues_num != 0:
autoproc_input.setNres(XSDataDouble(residues_num))
space_group = params.get("sample_reference").get("spacegroup", "")
if len(space_group) > 0:
autoproc_input.setSpacegroup(XSDataString(space_group))
unit_cell = params.get("sample_reference").get("cell", "")
if len(unit_cell) > 0:
autoproc_input.setUnit_cell(XSDataString(unit_cell))
autoproc_input.setCc_half_cutoff(XSDataDouble(18.0))
#Maybe we have to check if directory is there.
#Maybe create dir with mxcube
xds_appeared = False
wait_xds_start = time.time()
logging.debug("EMBLAutoprocessing: Waiting for XDS.INP " +\
"file: %s" % autoproc_xds_filename)
while not xds_appeared and time.time(
) - wait_xds_start < xds_input_file_wait_timeout:
if os.path.exists(autoproc_xds_filename) and \
os.stat(autoproc_xds_filename).st_size > 0:
xds_appeared = True
logging.debug('EMBLAutoprocessing: XDS.INP file is there, size={0}'.\
format(os.stat(autoproc_xds_filename).st_size))
else:
os.system("ls %s> /dev/null" %
(os.path.dirname(autoproc_path)))
gevent.sleep(xds_input_file_wait_resolution)
if not xds_appeared:
logging.error("EMBLAutoprocessing: XDS.INP file ({0}) failed " +\
"to appear after {1} seconds".\
format(autoproc_xds_filename, xds_input_file_wait_timeout))
return None, False
autoproc_input.exportToFile(autoproc_input_filename)
return autoproc_input_filename, True
def create_autoproc_input(self, event, params):
"""
Descript. :
"""
WAIT_XDS_TIMEOUT = 20
WAIT_XDS_RESOLUTION = 1
file_name_timestamp = time.strftime("%Y%m%d_%H%M%S")
autoproc_path = params.get("xds_dir")
autoproc_xds_filename = os.path.join(autoproc_path, "XDS.INP")
autoproc_input_filename = os.path.join(
autoproc_path, "edna-autoproc-input-%s" % file_name_timestamp
)
autoproc_output_file_name = os.path.join(
autoproc_path, "edna-autoproc-results-%s" % file_name_timestamp
)
autoproc_input = XSDataAutoprocInput()
autoproc_xds_file = XSDataFile()
autoproc_xds_file.setPath(XSDataString(autoproc_xds_filename))
autoproc_input.setInput_file(autoproc_xds_file)
autoproc_output_file = XSDataFile()
autoproc_output_file.setPath(XSDataString(autoproc_output_file_name))
autoproc_input.setOutput_file(autoproc_output_file)
autoproc_input.setData_collection_id(XSDataInteger(params.get("collection_id")))
residues_num = float(params.get("residues", 0))
if residues_num != 0:
autoproc_input.setNres(XSDataDouble(residues_num))
space_group = params.get("sample_reference").get("spacegroup", "")
if not isinstance(space_group, int) and len(space_group) > 0:
autoproc_input.setSpacegroup(XSDataString(space_group))
unit_cell = params.get("sample_reference").get("cell", "")
if len(unit_cell) > 0:
autoproc_input.setUnit_cell(XSDataString(unit_cell))
autoproc_input.setCc_half_cutoff(XSDataDouble(18.0))
# Maybe we have to check if directory is there. Maybe create dir with mxcube
xds_appeared = False
wait_xds_start = time.time()
logging.info(
"MAXIVAutoprocessing: Waiting for XDS.INP file: %s" % autoproc_xds_filename
)
while not xds_appeared and time.time() - wait_xds_start < WAIT_XDS_TIMEOUT:
if (
os.path.exists(autoproc_xds_filename)
and os.stat(autoproc_xds_filename).st_size > 0
):
xds_appeared = True
logging.debug(
"MAXIVAutoprocessing: XDS.INP file is there, size={0}".format(
os.stat(autoproc_xds_filename).st_size
)
)
else:
os.system("ls %s> /dev/null" % (os.path.dirname(autoproc_path)))
gevent.sleep(WAIT_XDS_RESOLUTION)
if not xds_appeared:
logging.error(
"MAXIVAutoprocessing: XDS.INP file ({0}) failed to appear after {1} seconds".format(
autoproc_xds_filename, WAIT_XDS_TIMEOUT
)
)
return None, False
autoproc_input.exportToFile(autoproc_input_filename)
return autoproc_input_filename, True
def create_input_files(self, xds_dir, mosflm_dir, dc_pars):
fileinfo = dc_pars["fileinfo"]
osc_seq = dc_pars["oscillation_sequence"][0]
prefix = fileinfo["prefix"]
runno = fileinfo["run_number"]
exp_time = osc_seq["exposure_time"]
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
start_img_num = osc_seq["start_image_number"]
angle_increment = osc_seq["range"]
wavelength = osc_seq.get("wavelength", 0)
xds_template_name = "XDS_TEMPLATE.INP"
mosflm_template_name = "mosflm_template.dat"
xds_template_path = os.path.join(self.template_dir, xds_template_name)
mosflm_template_path = os.path.join(self.template_dir,
mosflm_template_name)
xds_file = os.path.join(xds_dir, "XDS.INP")
mosflm_file = os.path.join(mosflm_dir, "mosflm.dat")
t = datetime.now()
# PREPARE VARIABLES
detsamdis = self.var_ds.detsamdis
beamx, beamy = self.var_ds.beamx, self.var_ds.beamy
mbeamx, mbeamy = beamy * 0.172, beamx * 0.172
datarangestartnum = start_img_num
datarangefinishnum = start_img_num + nb_images - 1
backgroundrangestartnum = start_img_num
spotrangestartnum = start_img_num
if angle_increment != 0:
minimumrange = int(round(20 / angle_increment))
elif angle_increment == 0:
minimumrange = 1
if nb_images >= minimumrange:
backgroundrangefinishnum = start_img_num + minimumrange - 1
if nb_images >= minimumrange:
spotrangefinishnum = start_img_num + minimumrange - 1
if nb_images < minimumrange:
backgroundrangefinishnum = start_img_num + nb_images - 1
if nb_images < minimumrange:
spotrangefinishnum = start_img_num + nb_images - 1
testlowres = 8.0
largestvector = (0.172 * ((max(beamx, 2463 - beamx))**2 +
(max(beamy, 2527 - beamy))**2)**0.5)
testhighres = round(
wavelength /
(2 * math.sin(0.5 * math.atan(largestvector / detsamdis))), 2)
lowres = 50.0
highres = testhighres
datafilename = prefix + "_" + str(runno) + "_????"
mdatafilename = prefix + "_" + str(runno) + "_####.cbf"
seconds = 5 * exp_time
if angle_increment < 1 and not angle_increment == 0:
seconds = 5 * exp_time / angle_increment
# DEFINE SG/UNIT CELL
spacegroupnumber = ""
unitcellconstants = ""
datapath_dir = os.path.abspath(xds_file).replace(
"PROCESS_DATA", "RAW_DATA")
datapath_dir = os.path.dirname(
os.path.dirname(datapath_dir)) + os.path.sep
# CREATE XDS.INP FILE
xds_templ = open(xds_template_path, "r").read()
xds_templ = xds_templ.replace("###BEAMX###", str(round(beamx, 2)))
xds_templ = xds_templ.replace("###BEAMY###", str(round(beamy, 2)))
xds_templ = xds_templ.replace("###DETSAMDIS###",
str(round(detsamdis, 2)))
xds_templ = xds_templ.replace("###ANGLEINCREMENT###",
str(angle_increment))
xds_templ = xds_templ.replace("###WAVELENGTH###", str(wavelength))
xds_templ = xds_templ.replace("###DATARANGESTARTNUM###",
str(datarangestartnum))
xds_templ = xds_templ.replace("###DATARANGEFINISHNUM###",
str(datarangefinishnum))
xds_templ = xds_templ.replace("###BACKGROUNDRANGESTART###",
str(backgroundrangestartnum))
xds_templ = xds_templ.replace("###BACKGROUNDRANGEFINISHNUM###",
str(backgroundrangefinishnum))
xds_templ = xds_templ.replace("###SPOTRANGESTARTNUM###",
str(spotrangestartnum))
xds_templ = xds_templ.replace("###SPOTRANGEFINISHNUM###",
str(spotrangefinishnum))
xds_templ = xds_templ.replace("###TESTLOWRES###", str(testlowres))
xds_templ = xds_templ.replace("###TESTHIGHRES###", str(testhighres))
xds_templ = xds_templ.replace("###LOWRES###", str(lowres))
xds_templ = xds_templ.replace("###HIGHRES###", str(highres))
xds_templ = xds_templ.replace("###DIRECTORY###", str(datapath_dir))
xds_templ = xds_templ.replace("###FILENAME###", str(datafilename))
xds_templ = xds_templ.replace("###SECONDS###", str(int(seconds)))
xds_templ = xds_templ.replace("###LYSOZYME_SPACE_GROUP_NUMBER###",
str(spacegroupnumber))
xds_templ = xds_templ.replace("###LYSOZYME_UNIT_CELL_CONSTANTS###",
str(unitcellconstants))
open(xds_file, "w").write(xds_templ)
# CREATE MOSFLM.DAT FILE
mosflm_templ = open(mosflm_template_path, "r").read()
mosflm_templ = mosflm_templ.replace("###DETSAMDIS###",
str(round(detsamdis, 2)))
mosflm_templ = mosflm_templ.replace("###BEAMX###",
str(round(mbeamx, 2)))
mosflm_templ = mosflm_templ.replace("###BEAMY###",
str(round(mbeamy, 2)))
mosflm_templ = mosflm_templ.replace("###DIRECTORY###",
str(datapath_dir))
mosflm_templ = mosflm_templ.replace("###FILENAME###",
str(mdatafilename))
mosflm_templ = mosflm_templ.replace("###WAVELENGTH###",
str(wavelength))
mosflm_templ = mosflm_templ.replace("###DATARANGESTARTNUM###",
str(datarangestartnum))
open(mosflm_file, "w").write(mosflm_templ)
# CREATE EDNAPROC XML FILE
collection_id = dc_pars["collection_id"]
output_dir = dc_pars["ednaproc_dir"]
ednaproc_input_file = os.path.join(
output_dir, "EDNAprocInput_%d.xml" % collection_id)
ednaproc_input = XSDataAutoprocInput()
input_file = XSDataFile()
path = XSDataString()
path.set_value(xds_file)
input_file.setPath(path)
ednaproc_input.setInput_file(input_file)
ednaproc_input.setData_collection_id(XSDataInteger(collection_id))
# output_dir = XSDataFile()
# outpath = XSDataString()
# outpath.set_value(output_dir)
# output_dir.setPath(path)
# ednaproc_input.setOutput_directory( output_dir )
ednaproc_input.exportToFile(ednaproc_input_file)
self.input_file = ednaproc_input_file
def create_input_files(self, xds_dir, mosflm_dir, dc_pars):
fileinfo = dc_pars["fileinfo"]
osc_seq = dc_pars["oscillation_sequence"][0]
prefix = fileinfo["prefix"]
runno = fileinfo["run_number"]
exp_time = osc_seq["exposure_time"]
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
start_img_num = osc_seq["start_image_number"]
angle_increment = osc_seq["range"]
wavelength = osc_seq.get("wavelength", 0)
xds_template_name = "XDS_TEMPLATE.INP"
mosflm_template_name = "mosflm_template.dat"
xds_template_path = os.path.join(self.template_dir, xds_template_name)
mosflm_template_path = os.path.join(self.template_dir, mosflm_template_name)
xds_file = os.path.join(xds_dir, "XDS.INP")
mosflm_file = os.path.join(mosflm_dir, "mosflm.dat")
t = datetime.now()
# PREPARE VARIABLES
detsamdis = self.var_ds.detsamdis
beamx, beamy = self.var_ds.beamx, self.var_ds.beamy
mbeamx, mbeamy = beamy * 0.172, beamx * 0.172
datarangestartnum = start_img_num
datarangefinishnum = start_img_num + nb_images - 1
backgroundrangestartnum = start_img_num
spotrangestartnum = start_img_num
if angle_increment != 0:
minimumrange = int(round(20 / angle_increment))
elif angle_increment == 0:
minimumrange = 1
if nb_images >= minimumrange:
backgroundrangefinishnum = start_img_num + minimumrange - 1
if nb_images >= minimumrange:
spotrangefinishnum = start_img_num + minimumrange - 1
if nb_images < minimumrange:
backgroundrangefinishnum = start_img_num + nb_images - 1
if nb_images < minimumrange:
spotrangefinishnum = start_img_num + nb_images - 1
testlowres = 8.0
largestvector = (
0.172
* ((max(beamx, 2463 - beamx)) ** 2 + (max(beamy, 2527 - beamy)) ** 2) ** 0.5
)
testhighres = round(
wavelength / (2 * math.sin(0.5 * math.atan(largestvector / detsamdis))), 2
)
lowres = 50.0
highres = testhighres
datafilename = prefix + "_" + str(runno) + "_????"
mdatafilename = prefix + "_" + str(runno) + "_####.cbf"
seconds = 5 * exp_time
if angle_increment < 1 and not angle_increment == 0:
seconds = 5 * exp_time / angle_increment
# DEFINE SG/UNIT CELL
spacegroupnumber = ""
unitcellconstants = ""
datapath_dir = os.path.abspath(xds_file).replace("PROCESS_DATA", "RAW_DATA")
datapath_dir = os.path.dirname(os.path.dirname(datapath_dir)) + os.path.sep
# CREATE XDS.INP FILE
xds_templ = open(xds_template_path, "r").read()
xds_templ = xds_templ.replace("###BEAMX###", str(round(beamx, 2)))
xds_templ = xds_templ.replace("###BEAMY###", str(round(beamy, 2)))
xds_templ = xds_templ.replace("###DETSAMDIS###", str(round(detsamdis, 2)))
xds_templ = xds_templ.replace("###ANGLEINCREMENT###", str(angle_increment))
xds_templ = xds_templ.replace("###WAVELENGTH###", str(wavelength))
xds_templ = xds_templ.replace("###DATARANGESTARTNUM###", str(datarangestartnum))
xds_templ = xds_templ.replace(
"###DATARANGEFINISHNUM###", str(datarangefinishnum)
)
xds_templ = xds_templ.replace(
"###BACKGROUNDRANGESTART###", str(backgroundrangestartnum)
)
xds_templ = xds_templ.replace(
"###BACKGROUNDRANGEFINISHNUM###", str(backgroundrangefinishnum)
)
xds_templ = xds_templ.replace("###SPOTRANGESTARTNUM###", str(spotrangestartnum))
xds_templ = xds_templ.replace(
"###SPOTRANGEFINISHNUM###", str(spotrangefinishnum)
)
xds_templ = xds_templ.replace("###TESTLOWRES###", str(testlowres))
xds_templ = xds_templ.replace("###TESTHIGHRES###", str(testhighres))
xds_templ = xds_templ.replace("###LOWRES###", str(lowres))
xds_templ = xds_templ.replace("###HIGHRES###", str(highres))
xds_templ = xds_templ.replace("###DIRECTORY###", str(datapath_dir))
xds_templ = xds_templ.replace("###FILENAME###", str(datafilename))
xds_templ = xds_templ.replace("###SECONDS###", str(int(seconds)))
xds_templ = xds_templ.replace(
"###LYSOZYME_SPACE_GROUP_NUMBER###", str(spacegroupnumber)
)
xds_templ = xds_templ.replace(
"###LYSOZYME_UNIT_CELL_CONSTANTS###", str(unitcellconstants)
)
open(xds_file, "w").write(xds_templ)
# CREATE MOSFLM.DAT FILE
mosflm_templ = open(mosflm_template_path, "r").read()
mosflm_templ = mosflm_templ.replace("###DETSAMDIS###", str(round(detsamdis, 2)))
mosflm_templ = mosflm_templ.replace("###BEAMX###", str(round(mbeamx, 2)))
mosflm_templ = mosflm_templ.replace("###BEAMY###", str(round(mbeamy, 2)))
mosflm_templ = mosflm_templ.replace("###DIRECTORY###", str(datapath_dir))
mosflm_templ = mosflm_templ.replace("###FILENAME###", str(mdatafilename))
mosflm_templ = mosflm_templ.replace("###WAVELENGTH###", str(wavelength))
mosflm_templ = mosflm_templ.replace(
"###DATARANGESTARTNUM###", str(datarangestartnum)
)
open(mosflm_file, "w").write(mosflm_templ)
# CREATE EDNAPROC XML FILE
collection_id = dc_pars["collection_id"]
output_dir = dc_pars["ednaproc_dir"]
ednaproc_input_file = os.path.join(
output_dir, "EDNAprocInput_%d.xml" % collection_id
)
ednaproc_input = XSDataAutoprocInput()
input_file = XSDataFile()
path = XSDataString()
path.setValue(xds_file)
input_file.setPath(path)
ednaproc_input.setInput_file(input_file)
ednaproc_input.setData_collection_id(XSDataInteger(collection_id))
# output_dir = XSDataFile()
# outpath = XSDataString()
# outpath.setValue(output_dir)
# output_dir.setPath(path)
# ednaproc_input.setOutput_directory( output_dir )
ednaproc_input.exportToFile(ednaproc_input_file)
self.input_file = ednaproc_input_file
def create_autoproc_input(self, event, params):
"""Creates processing input xml
:param event: processing type (after, before, image)
:type event: str
:param params: collection parameters
:type params: dict
"""
xds_input_file_wait_timeout = 20
xds_input_file_wait_resolution = 1
file_name_timestamp = time.strftime("%Y%m%d_%H%M%S")
autoproc_path = params.get("xds_dir")
autoproc_xds_filename = os.path.join(autoproc_path, "XDS.INP")
autoproc_input_filename = os.path.join(\
autoproc_path,
"edna-autoproc-input-%s.xml" % \
file_name_timestamp)
autoproc_output_file_name = os.path.join(\
autoproc_path,
"edna-autoproc-results-%s.xml" % \
file_name_timestamp)
autoproc_input = XSDataAutoprocInput()
autoproc_xds_file = XSDataFile()
autoproc_xds_file.setPath(XSDataString(autoproc_xds_filename))
autoproc_input.setInput_file(autoproc_xds_file)
autoproc_output_file = XSDataFile()
autoproc_output_file.setPath(XSDataString(autoproc_output_file_name))
autoproc_input.setOutput_file(autoproc_output_file)
autoproc_input.setData_collection_id(\
XSDataInteger(params.get("collection_id")))
residues_num = float(params.get("residues", 0))
if residues_num != 0:
autoproc_input.setNres(XSDataDouble(residues_num))
space_group = params.get("sample_reference").get("spacegroup", "")
if len(space_group) > 0:
autoproc_input.setSpacegroup(XSDataString(space_group))
unit_cell = params.get("sample_reference").get("cell", "")
if len(unit_cell) > 0:
autoproc_input.setUnit_cell(XSDataString(unit_cell))
autoproc_input.setCc_half_cutoff(XSDataDouble(18.0))
#Maybe we have to check if directory is there.
#Maybe create dir with mxcube
xds_appeared = False
wait_xds_start = time.time()
logging.debug("EMBLAutoprocessing: Waiting for XDS.INP " +\
"file: %s" % autoproc_xds_filename)
while not xds_appeared and time.time() - wait_xds_start < xds_input_file_wait_timeout:
if os.path.exists(autoproc_xds_filename) and \
os.stat(autoproc_xds_filename).st_size > 0:
xds_appeared = True
logging.debug('EMBLAutoprocessing: XDS.INP file is there, size={0}'.\
format(os.stat(autoproc_xds_filename).st_size))
else:
os.system("ls %s> /dev/null"%(os.path.dirname(autoproc_path)))
gevent.sleep(xds_input_file_wait_resolution)
if not xds_appeared:
logging.error("EMBLAutoprocessing: XDS.INP file ({0}) failed " +\
"to appear after {1} seconds".\
format(autoproc_xds_filename, xds_input_file_wait_timeout))
return None, False
autoproc_input.exportToFile(autoproc_input_filename)
return autoproc_input_filename, True
def create_autoproc_input(self, event, params):
"""
Descript. :
"""
WAIT_XDS_TIMEOUT = 20
WAIT_XDS_RESOLUTION = 1
file_name_timestamp = time.strftime("%Y%m%d_%H%M%S")
autoproc_path = params.get("xds_dir")
autoproc_xds_filename = os.path.join(autoproc_path, "XDS.INP")
autoproc_input_filename = os.path.join(
autoproc_path, "edna-autoproc-input-%s" % file_name_timestamp
)
autoproc_output_file_name = os.path.join(
autoproc_path, "edna-autoproc-results-%s" % file_name_timestamp
)
autoproc_input = XSDataAutoprocInput()
autoproc_xds_file = XSDataFile()
autoproc_xds_file.setPath(XSDataString(autoproc_xds_filename))
autoproc_input.setInput_file(autoproc_xds_file)
autoproc_output_file = XSDataFile()
autoproc_output_file.setPath(XSDataString(autoproc_output_file_name))
autoproc_input.setOutput_file(autoproc_output_file)
autoproc_input.setData_collection_id(XSDataInteger(params.get("collection_id")))
residues_num = float(params.get("residues", 0))
if residues_num != 0:
autoproc_input.setNres(XSDataDouble(residues_num))
space_group = params.get("sample_reference").get("spacegroup", "")
if not isinstance(space_group, int) and len(space_group) > 0:
autoproc_input.setSpacegroup(XSDataString(space_group))
unit_cell = params.get("sample_reference").get("cell", "")
if len(unit_cell) > 0:
autoproc_input.setUnit_cell(XSDataString(unit_cell))
autoproc_input.setCc_half_cutoff(XSDataDouble(18.0))
# Maybe we have to check if directory is there. Maybe create dir with mxcube
xds_appeared = False
wait_xds_start = time.time()
logging.info(
"MAXIVAutoprocessing: Waiting for XDS.INP file: %s" % autoproc_xds_filename
)
while not xds_appeared and time.time() - wait_xds_start < WAIT_XDS_TIMEOUT:
if (
os.path.exists(autoproc_xds_filename)
and os.stat(autoproc_xds_filename).st_size > 0
):
xds_appeared = True
logging.debug(
"MAXIVAutoprocessing: XDS.INP file is there, size={0}".format(
os.stat(autoproc_xds_filename).st_size
)
)
else:
os.system("ls %s> /dev/null" % (os.path.dirname(autoproc_path)))
gevent.sleep(WAIT_XDS_RESOLUTION)
if not xds_appeared:
logging.error(
"MAXIVAutoprocessing: XDS.INP file ({0}) failed to appear after {1} seconds".format(
autoproc_xds_filename, WAIT_XDS_TIMEOUT
)
)
return None, False
autoproc_input.exportToFile(autoproc_input_filename)
return autoproc_input_filename, True