def get_array_properties(self, array_name, keytype="A"):
"""Return a Struct defining the properties of the FITS array in extension named `array_name`."""
with fits_open(self.filepath) as hdulist:
try:
array_name = self._array_name_to_hdu_index(array_name)
hdu = hdulist[array_name[1]]
except Exception:
return 'UNDEFINED'
generic_class = {
"IMAGEHDU" : "IMAGE",
"BINTABLEHDU" : "TABLE",
}.get(hdu.__class__.__name__.upper(), "UNKNOWN")
if generic_class in ["IMAGE","UNKNOWN"]:
typespec = hdu.data.dtype.name
column_names = None
else: # TABLE
dtype = hdu.data.dtype
typespec = {name.upper():str(dtype.fields[name][0]) for name in dtype.names}
column_names = [name.upper() for name in hdu.data.dtype.names]
return utils.Struct(
SHAPE = hdu.data.shape,
KIND = generic_class,
DATA_TYPE = typespec,
COLUMN_NAMES = column_names,
NAME = array_name[0],
EXTENSION = array_name[1],
DATA = hdu.data if (keytype == "D") else None
)
def __init__(self, context, refpath, crdscfg):
self._context = context
self._refpath = refpath
self._crdscfg = utils.Struct(crdscfg)
self.pipeline_exceptions = self._crdscfg.get("pipeline_exceptions", {})
self.pipeline_cfgs_to_steps = self._crdscfg.get("pipeline_cfgs_to_steps", {})
self.steps_to_reftypes = self._crdscfg.get("steps_to_reftypes", {})
def jpoll_pull_messages(key, since_id=None):
"""Return a list of jpoll json message objects from the channel associated
with `key` sent after datetime string `since` or since the last pull if
since is not specified.
"""
messages = []
for msg in S.jpoll_pull_messages(key, since_id):
decoded = utils.Struct(msg)
decoded.data = html.unescape(decoded.data)
messages.append(decoded)
return messages
def fail_if_existing_lock(self):
"""Issue a warning if self.locked_instrument is already locked."""
response = self.get("/lock_status/" + self.username + "/")
log.verbose("lock_status:", response)
json_dict = utils.Struct(response.json())
if (json_dict.name and (not json_dict.is_expired)
and (json_dict.type == "instrument")
and (json_dict.user == self.username)):
log.fatal_error(
"User", repr(self.username), "has already locked",
repr(json_dict.name),
". Failing to avert collisions. User --logout or logout on the website to bypass."
)
def create_submission(self):
"""Create a Submission object based on script / command-line parameters."""
return utils.Struct(
uploaded_files={
os.path.basename(filepath): filepath
for filepath in self.files
} if self.args.files else {},
description=self.args.description,
username=self.username,
creator_name=self.args.creator,
change_level=self.args.change_level,
auto_rename=not self.args.dont_auto_rename,
compare_old_reference=not self.args.dont_compare_old_reference,
submission_kind=self.args.submission_kind,
observatory=self.observatory,
pmap_mode=self.pmap_mode,
pmap_name=self.pmap_name,
agent="command-line-script")
def __init__(self, header):
"""Initialize this TypeSpec from dict `header`, enforcing requirments and creating suitable
defaults for missing fields.
"""
header = utils.Struct(header)
assert "suffix" in header
assert "text_descr" in header or header.filetype == "all"
if "tpn" not in header:
header.tpn = header.instrument.lower() + "_" + header.suffix + ".tpn"
if "ld_tpn" not in header:
header.ld_tpn = header.instrument.lower() + "_" + header.suffix + "_ld.tpn"
if "file_ext" not in header:
header.file_ext = ".fits"
if "unique_rowkeys" not in header:
header.unique_rowkeys = None
if "extra_keys" not in header:
header.extra_keys = None
super(TypeSpec, self).__init__(header.items())
def get_system_versions(master_version, context=None):
"""Return the versions Struct associated with cal s/w master_version as
defined by `context` which can be defined as "null", "none", or None to use
the default context, or with any other valid date based context specifier.
"""
return utils.Struct(S.get_system_versions(master_version, str(context)))
def get_submission_info(observatory, username):
"""Return configuration parameters needed for command line file submission
relative to the current server, observatory, and username.
"""
return utils.Struct(S.get_submission_info(observatory, username))
def get_affected_datasets(observatory, old_context=None, new_context=None):
"""Return a structure describing the ids affected by the last context change."""
return utils.Struct(S.get_affected_datasets(observatory, old_context, new_context))
def get_body(self):
"""Load the input_yaml as a CRDS Struct and return it."""
return utils.Struct(yaml.safe_load(self.input_yaml))
def __init__(self, context, refpath, crdscfg):
self._context = context
self._refpath = refpath
self._crdscfg = utils.Struct(crdscfg)
