class Provenance(object):
def __init__(self, output_dir):
self.output_dir = output_dir
self.doc = None
self.workflow = None
def start(self, workflow=False):
from daops import __version__ as daops_version
from housemartin import __version__ as housemartin_version
self.doc = ProvDocument()
# Declaring namespaces for various prefixes
self.doc.set_default_namespace(uri="http://purl.org/roocs/prov#")
self.doc.add_namespace("prov", uri="http://www.w3.org/ns/prov#")
self.doc.add_namespace(
"provone", uri="http://purl.dataone.org/provone/2015/01/15/ontology#"
)
self.doc.add_namespace("dcterms", uri="http://purl.org/dc/terms/")
# Define entities
project_cds = self.doc.agent(
":copernicus_CDS",
{
"prov:type": "prov:Organization",
"dcterms:title": "Copernicus Climate Data Store",
},
)
self.sw_housemartin = self.doc.agent(
":housemartin",
{
"prov:type": "prov:SoftwareAgent",
"dcterms:source": f"https://github.com/cedadev/housemartin/releases/tag/v{housemartin_version}",
},
)
self.doc.wasAttributedTo(self.sw_housemartin, project_cds)
self.sw_daops = self.doc.agent(
":daops",
{
"prov:type": "prov:SoftwareAgent",
"dcterms:source": f"https://github.com/roocs/daops/releases/tag/v{daops_version}",
},
)
# workflow
if workflow is True:
self.workflow = self.doc.entity(
":workflow", {"prov:type": "provone:Workflow"}
)
orchestrate = self.doc.activity(
":orchestrate",
other_attributes={
"prov:startedAtTime": "2020-11-26T09:15:00",
"prov:endedAtTime": "2020-11-26T09:30:00",
},
)
self.doc.wasAssociatedWith(
orchestrate, agent=self.sw_housemartin, plan=self.workflow
)
def add_operator(self, operator, parameters, collection, output):
op = self.doc.activity(
f":{operator}",
other_attributes={
":time": parameters.get("time"),
":apply_fixes": parameters.get("apply_fixes"),
},
)
# input data
ds_in = os.path.basename(collection[0])
# ds_in_attrs = {
# 'prov:type': 'provone:Data',
# 'prov:value': f'{ds_in}',
# }
op_in = self.doc.entity(f":{ds_in}")
# operator started by daops
if self.workflow:
self.doc.wasAssociatedWith(op, agent=self.sw_daops, plan=self.workflow)
else:
self.doc.start(op, starter=self.sw_daops, trigger=self.sw_housemartin)
# Generated output file
ds_out = os.path.basename(output[0])
# ds_out_attrs = {
# 'prov:type': 'provone:Data',
# 'prov:value': f'{ds_out}',
# }
op_out = self.doc.entity(f":{ds_out}")
self.doc.wasDerivedFrom(op_out, op_in, activity=op)
def write_json(self):
outfile = os.path.join(self.output_dir, "provenance.json")
self.doc.serialize(outfile, format="json")
return outfile
def write_png(self):
outfile = os.path.join(self.output_dir, "provenance.png")
figure = prov_to_dot(self.doc)
figure.write_png(outfile)
return outfile
