def write_parameters(data, run_dir, is_parallel):
rtfile = py.path.local(_parent_file(run_dir, RTSTRUCT_EXPORT_FILENAME))
if data['report'] == 'dvhReport' and rtfile.exists():
return
if data['report'] in ('doseCalculation', 'dvhReport'):
_, roi_models = _generate_rtstruct_file(_parent_dir(run_dir),
_parent_dir(run_dir))
if data['report'] == 'doseCalculation':
dose_calc = data.models.doseCalculation
roi_data = roi_models['regionsOfInterest']
ptv_name = ''
oar_names = []
for roi_number in roi_data:
if roi_number == dose_calc.selectedPTV:
ptv_name = roi_data[roi_number]['name']
elif roi_number in dose_calc.selectedOARs:
oar_names.append(roi_data[roi_number]['name'])
prescription = run_dir.join(PRESCRIPTION_FILENAME)
simulation_db.write_json(prescription, {
'ptv': ptv_name,
'oar': oar_names,
})
pkjinja.render_file(
RESOURCE_DIR.join(DOSE_CALC_SH + '.jinja'),
{
'prescription': prescription,
'beamlist': run_dir.join(_BEAMLIST_FILENAME),
'dicom_zip': _sim_file(data['simulationId'],
_ZIP_FILE_NAME),
},
output=run_dir.join(DOSE_CALC_SH),
strict_undefined=True,
),
def write_parameters(data, run_dir, is_parallel):
rtfile = py.path.local(_parent_file(run_dir, RTSTRUCT_EXPORT_FILENAME))
if data['report'] == 'dvhReport' and rtfile.exists():
return
if data['report'] in ('doseCalculation', 'dvhReport'):
_, roi_models = _generate_rtstruct_file(_parent_dir(run_dir), _parent_dir(run_dir))
if data['report'] == 'doseCalculation':
dose_calc = data.models.doseCalculation
roi_data = roi_models['regionsOfInterest']
ptv_name = ''
oar_names = []
for roi_number in roi_data:
if roi_number == dose_calc.selectedPTV:
ptv_name = roi_data[roi_number]['name']
elif roi_number in dose_calc.selectedOARs:
oar_names.append(roi_data[roi_number]['name'])
prescription = run_dir.join(PRESCRIPTION_FILENAME)
simulation_db.write_json(
prescription,
{
'ptv': ptv_name,
'oar': oar_names,
})
pkjinja.render_file(
RESOURCE_DIR.join(DOSE_CALC_SH + '.jinja'),
{
'prescription': prescription,
'beamlist': run_dir.join(_BEAMLIST_FILENAME),
'dicom_zip': _sim_file(data['simulationId'], _ZIP_FILE_NAME),
},
output=run_dir.join(DOSE_CALC_SH),
strict_undefined=True,
),
def __init__(self, *args, **kwargs):
super(T, self).__init__(*args, **kwargs)
self.root_d = pkio.py_path(cfg.root_d)
self.db_d = self.root_d.join(DB_SUBDIR)
self.proprietary_source_d = self.root_d.join(PROPRIETARY_SUBDIR)
self.rpm_source_d = self.root_d.join(RPM_SUBDIR)
self.tmp_d = self.root_d.join(TMP_SUBDIR)
self.secret_d = self.db_d.join(SECRET_SUBDIR)
self.srv_d = self.root_d.join(SRV_SUBDIR)
self.srv_host_d = self.srv_d.join(HOST_SUBDIR)
self.base = PKDict()
f = None
try:
for d in self.db_d, self.secret_d:
for f in pkio.sorted_glob(d.join(ZERO_YML)):
v = pkyaml.load_str(
pkjinja.render_file(
f,
self.base,
strict_undefined=True,
),
)
merge_dict(self.base, v)
except Exception:
pkdlog('error rendering db={}', f)
raise
def _render_file(self, path, j2_ctx):
from pykern import pkjinja
try:
return pkjinja.render_file(path, j2_ctx, strict_undefined=True)
except Exception as e:
pkdlog('path={} exception={}', path, e)
raise
def render_jinja(sim_type, v, name=PARAMETERS_PYTHON_FILE):
"""Render the values into a jinja template.
Args:
sim_type (str): application name
v: flattened model data
Returns:
str: source text
"""
b = resource_dir(sim_type).join(name)
return pkjinja.render_file(b + '.jinja', v)
def render_jinja(sim_type, v, name=PARAMETERS_PYTHON_FILE):
"""Render the values into a jinja template.
Args:
sim_type (str): application name
v: flattened model data
Returns:
str: source text
"""
d = sirepo.sim_data.get_class(sim_type).resource_dir() if sim_type \
else sirepo.sim_data.resource_dir()
return pkjinja.render_file(
# append .jinja, because file may already have an extension
d.join(name) + '.jinja',
v,
)
def render_static_jinja(base, ext, j2_ctx, cache_ok=False):
"""Render static template with jinja
Args:
base (str): base name of file, e.g. ``user-state``
ext (str): suffix of file, e.g. ``js``
j2_ctx (dict): jinja context
cache_ok (bool): OK to cache the result? [default: False]
Returns:
Flask.Response: reply
"""
p = simulation_db.STATIC_FOLDER.join('{}/{}.{}'.format(ext, base, ext))
r = flask.Response(
pkjinja.render_file(p, j2_ctx, strict_undefined=True),
mimetype=MIME_TYPE[ext],
)
if cache_ok:
return headers_for_cache(r, path=p)
return headers_for_no_cache(r)
def _render(*args, **kwargs):
"""Renders the template and adds to git"""
pkjinja.render_file(*args, **kwargs)
subprocess.check_call(['git', 'add', kwargs['output']])
def default_command():
import rsconf.component
import rsconf.component.rsconf
import rsconf.pkcli.tls
root_d = db.cfg.root_d
if root_d.check():
return '{}: already exists'.format(root_d)
srv = pkio.mkdir_parent(root_d.join(db.SRV_SUBDIR))
def _sym(old, new_base=None):
old = pkio.py_path(old)
if not new_base:
new_base = old.basename
assert old.check(), \
'{}: does not exist'.format(old)
srv.join(new_base).mksymlinkto(old, absolute=False)
# ssh-keygen -q -N '' -C rsconf -t rsa -b 4096 -f /var/tmp/foo
# -- don't need this
db_d = pkio.mkdir_parent(root_d.join(db.DB_SUBDIR))
secret_d = pkio.mkdir_parent(db_d.join(db.SECRET_SUBDIR))
nginx_d = pkio.mkdir_parent(root_d.join(NGINX_SUBDIR))
boot_hdb = pkcollections.Dict(rsconf_db=pkcollections.Dict(
secret_d=secret_d,
channel='dev',
))
j2_ctx = pkcollections.Dict(
all_host='v9.radia.run',
group=grp.getgrgid(os.getgid())[0],
host='v4.radia.run',
master='v3.radia.run',
port=2916,
root_d=root_d,
srv_d=str(srv),
uid=os.getuid(),
user=pwd.getpwuid(os.getuid())[0],
worker5_host='v5.radia.run',
worker6_host='v6.radia.run',
)
hosts = [h for h in j2_ctx.values() if str(h).endswith('.radia.run')]
# bootstrap
j2_ctx.update(boot_hdb)
j2_ctx.rsconf_db.http_host = 'http://{}:{}'.format(j2_ctx.master,
j2_ctx.port)
j2_ctx.bkp = pkcollections.Dict(primary=j2_ctx.host)
j2_ctx.passwd_f = rsconf.component.rsconf.passwd_secret_f(j2_ctx)
for h in hosts:
_add_host(j2_ctx, srv, h)
_sym('~/src/radiasoft/download/bin/install.sh', 'index.html')
_sym(pkresource.filename('rsconf/rsconf.sh'), 'rsconf.sh')
dev_d = pkio.py_path(pkresource.filename('dev'))
for f in pkio.walk_tree(dev_d):
if str(f).endswith('~') or str(f).startswith('#'):
continue
x = str(f.relto(dev_d))
if not ('local/' in x and x.endswith('.sh.jinja')):
x = re.sub('.jinja$', '', x)
dst = root_d.join(x)
pkio.mkdir_parent_only(dst)
if f.basename == dst.basename:
f.copy(dst)
else:
pkjinja.render_file(f, j2_ctx, output=dst, strict_undefined=True)
n = []
for e in 'rpm', 'proprietary':
d = pkio.py_path(root_d.dirname).join(e)
pkio.mkdir_parent(d)
root_d.join(e).mksymlinkto(d, absolute=False)
n.append(str(d))
subprocess.check_call(['bash', str(secret_d.join('setup_dev.sh')), *n], )
# dev only, really insecure, but makes consistent builds easy
_sym('~/src/radiasoft')
_sym('~/src/biviosoftware')
for h in hosts:
# needed to be able to talk setup certs for registry so we can
# pull private images from all hosts. Only used in dev, because
# private registry doesn't protect against pushes from these hosts.
if h != j2_ctx.master:
subprocess.check_call(
['rsconf', 'host', 'init_docker_registry', h])
tls_d = secret_d.join(rsconf.component.TLS_SECRET_SUBDIR)
tls_d.ensure(dir=True)
for h in (
'jupyter.' + j2_ctx.all_host,
'jupyter.' + j2_ctx.host,
j2_ctx.all_host,
j2_ctx.master,
j2_ctx.worker5_host,
j2_ctx.worker6_host,
):
rsconf.pkcli.tls.gen_self_signed_crt(
tls_d.join(h),
h,
)
rsconf.pkcli.tls.gen_self_signed_crt(
tls_d.join('star.' + j2_ctx.host),
'*.' + j2_ctx.host,
j2_ctx.host,
)