import datetime
import socket
import xml.etree.ElementTree as etree
from .serialize import serialize_metadata
from .. import __version__
ICAT_NAMESPACE_URL = "http://www.esrf.fr/icat"
etree.register_namespace("tns", ICAT_NAMESPACE_URL)
[docs]
def root_node(name: str, **kw):
return etree.Element(f"{{{ICAT_NAMESPACE_URL}}}{name}", **kw)
[docs]
def child_node(parent, name: str, **kw):
return etree.SubElement(parent, f"{{{ICAT_NAMESPACE_URL}}}{name}", **kw)
[docs]
def encode_node_data(data) -> str:
text = serialize_metadata(data)
if not isinstance(text, str):
raise ValueError(data)
return text
[docs]
def data_node(parent, name: str, data, **kw):
node = child_node(parent, name, **kw)
node.text = encode_node_data(data)
[docs]
def parameter_node(parent, name: str, value, **kw):
node = child_node(parent, "parameter", **kw)
data_node(node, "name", name)
data_node(node, "value", value)
[docs]
def dataset_as_xml(
beamline: str, proposal: str, dataset: str, path: str, metadata: dict = None
):
assert beamline, "ICAT requires the beamline name"
assert proposal, "ICAT requires the proposal name"
assert dataset, "ICAT requires the dataset name"
assert path, "ICAT requires the dataset path"
if metadata is None:
metadata = dict()
# Required metadata
assert "Sample_name" in metadata, "ICAT metadata field 'Sample_name' is missing"
# Metadata with defaults
if "startDate" not in metadata:
metadata["startDate"] = datetime.datetime.now().astimezone()
if "endDate" not in metadata:
metadata["endDate"] = datetime.datetime.now().astimezone()
metadata.setdefault("machine", socket.getfqdn())
metadata.setdefault("software", "pyicat-plus_v" + __version__)
root = root_node("dataset", attrib={"complete": "true"})
data_node(root, "investigation", proposal)
data_node(root, "instrument", beamline)
data_node(root, "name", dataset)
data_node(root, "location", path)
metadata = serialize_metadata(metadata)
for name, value in metadata.items():
parameter_node(root, name, value)
# Metadata included in the XML tree
if name == "Sample_name":
sample = child_node(root, "sample")
data_node(sample, "name", value)
elif name == "startDate":
data_node(root, "startDate", value)
elif name == "endDate":
data_node(root, "endDate", value)
return root
[docs]
def investigation_as_xml(
beamline: str, proposal: str, start_datetime=None, end_datetime=None
):
root = root_node("investigation")
data_node(root, "experiment", proposal)
data_node(root, "instrument", beamline)
if start_datetime is None:
start_datetime = datetime.datetime.now().astimezone()
data_node(root, "startDate", start_datetime)
if end_datetime is not None:
data_node(root, "endDate", end_datetime)
return root