def __init__(self, f_choices, sigf_choices, sg_num, *args, **kwargs):
super(MRForm, self).__init__(*args, **kwargs)
self.fields['f_value'].choices = f_choices
self.fields['sigf_value'].choices = sigf_choices
sgroups = utils.getGroupNumbersFromNumber(sg_num)
sg_choices = []
for sg in sgroups:
sg_choices.append((sg, utils.sgNumNameTrans(number=sg)))
self.fields['space_group'].choices = sg_choices
self.fields['space_group'].initial = \
(sg_num, utils.sgNumNameTrans(number=sg_num))
def makeJobScripts(self, request):
"""
create PBS/OGE job submission files, one for
each rmsd, pdb file and spacegroup
"""
time = "12:0:0"
pbs_prefix = "#$ "
pbs_head = "#!/bin/sh\n"
pbs_head += "%s-m abe\n" % pbs_prefix
pbs_head += "%s-S /bin/bash\n" % pbs_prefix
pbs_head += "%s-cwd\n" % pbs_prefix
pbs_head += "%s-l h_rt=%s\n" % (pbs_prefix, time)
pbs_commands = "\n. /etc/profile\n"
pbs_commands += "module load phenix\n"
pbs_commands += ". $PHENIX/build/$PHENIX_MTYPE/setpaths.sh\n"
pingurl = request.build_absolute_uri(
reverse('tardis.apps.mrtardis.views.jobfinished',
args=[self.dataset.id]))
wget_command = "wget -O - %s?jobid=$JOB_ID" % pingurl
## ping server ten times with more and more delay
pbs_footer = "touch jobid-$JOB_ID.finished\n"
pbs_footer += "I=0; while [[ \"true\" != `%s`" % wget_command
pbs_footer += "&& $I -lt 10 ]];"
pbs_footer += "do echo yes; sleep $(($I*2)); I=$(($I+1)); done"
#pbs_footer = wget_command
phaser_command = "phenix.phaser"
spacegroups = [utils.sgNumNameTrans(number=sgnum)
for sgnum in self.get_params("space_group", value=True)]
if self.get_param("sg_all", value=True) == "True":
spacegroups.append("ALL")
rmsds = self.get_params("rmsd", value=True)
for pdbfile in self.get_params("PDBfile", value=True):
for sg in spacegroups:
for rmsd in rmsds:
parameters = self.getPhaserCommands(sg,
rmsd,
pdbfile)
output = pbs_head + pbs_commands
output += "echo -e \"" + parameters + "\"|" +\
phaser_command + " \n"
output += pbs_footer
jobfilename = pdbfile + "_" + sg + "_" + \
str(rmsd) + ".jobfile"
ofile = open(os.path.join(
get_full_staging_path(request.user.username),
jobfilename), 'w')
ofile.write(output)
ofile.close()
utils.add_staged_file_to_dataset(
jobfilename,
self.dataset.id,
request.user.username,
mimetype="application/x-shellscript")
self.new_param("jobscript", jobfilename)
def makeJobScripts(self):
"""create PBS/OGE job submission files, one for
each pdb file and spacegroup"""
time = "12:0:0"
pbs_prefix = "#$ "
pbs_head = "#!/bin/sh\n"
pbs_head += pbs_prefix + "-m abe\n"
pbs_head += pbs_prefix + "-S /bin/bash\n"
pbs_head += pbs_prefix + "-cwd\n"
pbs_commands = """
. /etc/profile
module load phenix
. $PHENIX/build/$PHENIX_MTYPE/setpaths.sh
"""
pbs_options = pbs_prefix + "-l h_rt=" + time + "\n"
phaser_command = "phenix.phaser"
for pdbfile in glob.glob(self.tmpdir + "/*.pdb"):
pdbfile = os.path.basename(pdbfile)
if type(self.parameters["space_group"]).__name__ == 'string':
# ie. not list or tuple
spacegroups = [self.parameters["space_group"]]
else:
spacegroups = self.parameters["space_group"]
for sg_num in spacegroups:
if sg_num == "ALL":
space_group = "ALL"
else:
from tardis.apps.mrtardis.utils import sgNumNameTrans
space_group = sgNumNameTrans(number=sg_num)
if type(self.parameters["rmsd"]).__name__ != 'list':
# ie. not list or tuple
rmsds = [self.parameters["rmsd"]]
else:
rmsds = self.parameters["rmsd"]
for rmsd in rmsds:
#print pdbfile
parameters = self.preparePhaserInput(space_group,
rmsd, pdbfile)
output = pbs_head + pbs_options + pbs_commands
output += "echo -e \"" + parameters + "\"|" +\
phaser_command + " \n"
jobfilename = pdbfile + "_" + space_group + "_" + \
repr(rmsd) + ".jobfile"
ofile = open(self.tmpdir + "/" + jobfilename, 'w')
ofile.write(output)
ofile.close()
self.jobfiles.append(jobfilename)
def __init__(self, f_choices, sigf_choices, sg_num, *args, **kwargs):
"""
A custom initialiser which translates between spacegroup numbers
and names, and sets up choices for F and SIGF columns.
:param f_choices: list of choices for the F column
as taken from MTZ parser.
:type f_choices: list of strings
:param sigf_choices: list of choices for the SIGF column
as taken from MTZ parser.
:type sigf_choices: list of strings
:param sg_num: space group number taken from the MTZ parser
:type sg_num: integer
"""
super(ParamForm, self).__init__(*args, **kwargs)
self.fields["f_value"].choices = f_choices
self.fields["sigf_value"].choices = sigf_choices
sgroups = utils.getGroupNumbersFromNumber(sg_num)
sg_choices = [(sg, utils.sgNumNameTrans(number=sg)) for sg in sgroups]
self.fields["space_group"].choices = sg_choices
def MRParams(request, dataset_id):
"""
shows the parameter entry form,
takes request.GET["dataset_id"] as input.
"""
# return True
#dataset_id = request.GET["dataset_id"]
#getMTZfile
mtz_file = utils.get_mtz_file(dataset_id)
mtz_params = utils.processMTZ(mtz_file.get_storage_path())
tochoice = lambda x: (x, x)
f_choices = map(tochoice, mtz_params["f_value"])
sigf_choices = map(tochoice, mtz_params["sigf_value"])
sg_num = mtz_params["spacegroup"]
pdbfilelist = utils.get_pdb_files(dataset_id)
rmsd_formfactory = formset_factory(RmsdForm)
if request.method == 'POST':
logger.debug("we're POSTing")
param_form = MRForm(f_choices,
sigf_choices,
sg_num,
request.POST)
rmsd_formset = rmsd_formfactory(request.POST)
logger.debug(repr(param_form.is_valid()) +
repr(rmsd_formset.is_valid()) +
repr(rmsd_formset.errors) +
repr(request.POST))
if param_form.is_valid() and rmsd_formset.is_valid():
hpcUsername = MrTUser.objects.get(user=request.user).hpc_username
newJob = hpcjob.HPCJob(hpcUsername)
jobparameters = {
"f_value": param_form.cleaned_data['f_value'],
"sigf_value": param_form.cleaned_data['sigf_value'],
"num_in_asym": param_form.cleaned_data['num_in_asym'],
"ensemble_number": param_form.cleaned_data['ensemble_number'],
"packing": param_form.cleaned_data['packing'],
"space_group": param_form.cleaned_data['space_group'],
}
if "sg_all" in param_form.cleaned_data:
if param_form.cleaned_data["sg_all"] == True:
jobparameters["space_group"].append("ALL")
jobparameters["rmsd"] = []
for form in rmsd_formset.forms:
jobparameters["rmsd"].append(form.cleaned_data['rmsd'])
jobparameters["mol_weight"] = param_form.cleaned_data['mol_weight']
filepaths = utils.get_pdb_files(dataset_id,
storagePaths=True) + [mtz_file.get_storage_path()]
logger.debug("params: " + repr(jobparameters))
logger.debug("files: " + repr(filepaths))
newJob.stage(jobparameters, filepaths)
newJob.submit()
dataset = Dataset.objects.get(pk=dataset_id)
newJob.dbSave(dataset.experiment_id, dataset,
request.user)
c = Context({})
return render_to_response("mrtardis/running_job.html", c)
else:
param_form = MRForm(f_choices=f_choices,
sigf_choices=sigf_choices,
sg_num=sg_num)
rmsd_formset = rmsd_formfactory()
c = Context({
'dataset_id': dataset_id,
'mtz_params': mtz_params,
'rmsd_formset': rmsd_formset,
'paramForm': param_form,
'fileName': mtz_file.filename,
'pdbfilelist': pdbfilelist,
'spacegroupname': utils.sgNumNameTrans(number=sg_num),
})
return render_to_response("mrtardis/parameters.html", c)