def addFile(request, dataset_id):
import shutil
from tardis.apps.mrtardis.utils import add_staged_file_to_dataset
if "file_id" not in request.POST:
return HttpResponseNotFound()
file_id = request.POST["file_id"]
file = Dataset_File.objects.get(pk=file_id)
shutil.copy(file.get_absolute_filepath(), get_full_staging_path(request.user.username))
add_staged_file_to_dataset(file.filename, dataset_id, request.user.username, file.mimetype)
return parseMTZfile(request, dataset_id=dataset_id)
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 retrieveFromHPC(self, location="msg"):
if self.get_status(value=True) != "readyToRetrieve":
return False
hpc_username = self.get_param("hpc_username", value=True)
user = HPCUser.objects.get(hpc_username=hpc_username)
excludefiles = self.get_params("uploaded_file", value=True)
hpclink = self.connectToHPC(location, hpc_username)
newfiles = hpclink.download(self.get_hpc_dir(),
get_full_staging_path(user.user.username),
excludefiles=excludefiles)
for newfile in newfiles:
add_staged_file_to_dataset(newfile, self.dataset.id,
user.user.username)
hpclink.rmtree(self.get_hpc_dir())
self.set_status("finished")
return True
def extractPDBzips(self, username):
"""
Extracts pdb files out of zips, adds them to the dataset and
removes the zip.
"""
zipquery = Dataset_File.objects.filter(dataset=self.dataset,
filename__iendswith=".zip")
for zipfileobj in zipquery:
zippath = zipfileobj.get_absolute_filepath()
thiszip = zipfile.ZipFile(zippath, 'r')
extractlist = []
for filename in thiszip.namelist():
if filename.endswith((".pdb", ".PDB")) and \
not filename.startswith("__MACOSX"):
extractlist.append(filename)
thiszip.extractall(get_full_staging_path(username), extractlist)
thiszip.close()
for pdbfile in extractlist:
#print pdbfile
utils.add_staged_file_to_dataset(
pdbfile, self.dataset.id, username,
mimetype="chemical/x-pdb")
zipfileobj.deleteCompletely()
