def get_provenance_history(uuid, normalized_provenance_dict):
prov_doc = ProvDocument()
# The 'prov' prefix is build-in namespace, no need to redefine here
prov_doc.add_namespace(HUBMAP_NAMESPACE, 'https://hubmapconsortium.org/')
# A bit validation
if 'relationships' not in normalized_provenance_dict:
raise LookupError(
f'Missing "relationships" key from the normalized_provenance_dict for Entity of uuid: {uuid}'
)
if 'nodes' not in normalized_provenance_dict:
raise LookupError(
f'Missing "nodes" key from the normalized_provenance_dict for Entity of uuid: {uuid}'
)
# Pack the nodes into a dictionary using the uuid as key
nodes_dict = {}
for node in normalized_provenance_dict['nodes']:
nodes_dict[node['uuid']] = node
# Loop through the relationships and build the provenance document
for rel_dict in normalized_provenance_dict['relationships']:
# (Activity) - [ACTIVITY_OUTPUT] -> (Entity)
if rel_dict['rel_data']['type'] == 'ACTIVITY_OUTPUT':
activity_uuid = rel_dict['fromNode']['uuid']
entity_uuid = rel_dict['toNode']['uuid']
# (Entity) - [ACTIVITY_INPUT] -> (Activity)
elif rel_dict['rel_data']['type'] == 'ACTIVITY_INPUT':
entity_uuid = rel_dict['fromNode']['uuid']
activity_uuid = rel_dict['toNode']['uuid']
activity_node = nodes_dict[activity_uuid]
entity_node = nodes_dict[entity_uuid]
activity_uri = None
entity_uri = None
# Skip Lab nodes for agent and organization
if entity_node['entity_type'] != 'Lab':
# Get the agent information from the entity node
agent_record = get_agent_record(entity_node)
# Use 'created_by_user_sub' as agent ID if presents
# Otherwise, fall back to use email by replacing @ and .
created_by_user_sub_prov_key = f'{HUBMAP_NAMESPACE}:userUUID'
created_by_user_email_prov_key = f'{HUBMAP_NAMESPACE}:userEmail'
if created_by_user_sub_prov_key in agent_record:
agent_id = agent_record[created_by_user_sub_prov_key]
elif created_by_user_email_prov_key in agent_record:
agent_id = str(
agent_record[created_by_user_email_prov_key]).replace(
'@', '-')
agent_id = str(agent_id).replace('.', '-')
else:
msg = f"Both 'created_by_user_sub' and 'created_by_user_email' are missing form entity of uuid: {entity_node['uuid']}"
logger.error(msg)
raise LookupError(msg)
# Build the agent uri
agent_uri = build_uri(HUBMAP_NAMESPACE, 'agent', agent_id)
# Only add the same agent once
# Multiple entities can be associated to the same agent
agent = prov_doc.get_record(agent_uri)
if len(agent) == 0:
doc_agent = prov_doc.agent(agent_uri, agent_record)
else:
doc_agent = agent[0]
# Organization
# Get the organization information from the entity node
org_record = get_organization_record(entity_node)
# Build the organization uri
group_uuid_prov_key = f'{HUBMAP_NAMESPACE}:groupUUID'
org_uri = build_uri(HUBMAP_NAMESPACE, 'organization',
org_record[group_uuid_prov_key])
# Only add the same organization once
# Multiple entities can be associated to different agents who are from the same organization
org = prov_doc.get_record(org_uri)
if len(org) == 0:
doc_org = prov_doc.agent(org_uri, org_record)
else:
doc_org = org[0]
# Build the activity uri
activity_uri = build_uri(HUBMAP_NAMESPACE, 'activities',
activity_node['uuid'])
# Register activity if not already registered
activity = prov_doc.get_record(activity_uri)
if len(activity) == 0:
# Shared attributes to be added to the PROV document
activity_attributes = {'prov:type': 'Activity'}
# Convert the timestampt integer to datetime string
# Note: in our case, prov:startTime is the same as prov:endTime
activity_time = timestamp_to_datetime(
activity_node['created_timestamp'])
# Add prefix to all other attributes
for key in activity_node:
prov_key = f'{HUBMAP_NAMESPACE}:{key}'
# Use datetime string instead of timestamp integer
if key == 'created_timestamp':
activity_attributes[prov_key] = activity_time
else:
activity_attributes[prov_key] = activity_node[key]
# Register activity
doc_activity = prov_doc.activity(activity_uri, activity_time,
activity_time,
activity_attributes)
# Relationship: the agent actedOnBehalfOf the org
prov_doc.actedOnBehalfOf(doc_agent, doc_org, doc_activity)
else:
doc_activity = activity[0]
# Build the entity uri
entity_uri = build_uri(HUBMAP_NAMESPACE, 'entities',
entity_node['uuid'])
# Register entity is not already registered
if len(prov_doc.get_record(entity_uri)) == 0:
# Shared attributes to be added to the PROV document
entity_attributes = {'prov:type': 'Entity'}
# Add prefix to all other attributes
for key in entity_node:
# Entity property values can be list or dict, skip
# And list and dict are unhashable types when calling `prov_doc.entity()`
if not isinstance(entity_node[key], (list, dict)):
prov_key = f'{HUBMAP_NAMESPACE}:{key}'
# Use datetime string instead of timestamp integer
if key in [
'created_timestamp', 'last_modified_timestamp',
'published_timestamp'
]:
entity_attributes[prov_key] = activity_time
else:
entity_attributes[prov_key] = entity_node[key]
# Register entity
prov_doc.entity(entity_uri, entity_attributes)
# Build activity uri and entity uri if not already built
# For the Lab nodes
if activity_uri is None:
activity_uri = build_uri(HUBMAP_NAMESPACE, 'activities',
activity_node['uuid'])
if entity_uri is None:
entity_uri = build_uri(HUBMAP_NAMESPACE, 'entities',
entity_node['uuid'])
# The following relationships apply to all node including Lab entity nodes
# (Activity) - [ACTIVITY_OUTPUT] -> (Entity)
if rel_dict['rel_data']['type'] == 'ACTIVITY_OUTPUT':
# Relationship: the entity wasGeneratedBy the activity
prov_doc.wasGeneratedBy(entity_uri, activity_uri)
# (Entity) - [ACTIVITY_INPUT] -> (Activity)
elif rel_dict['rel_data']['type'] == 'ACTIVITY_INPUT':
# Relationship: the activity used the entity
prov_doc.used(activity_uri, entity_uri)
# Format into json string based on the PROV-JSON Serialization
# https://www.w3.org/Submission/prov-json/
serialized_json = prov_doc.serialize()
return serialized_json
class ProvenanceProfile:
"""
Provenance profile.
Populated as the workflow runs.
"""
def __init__(
self,
research_object: "ResearchObject",
full_name: str,
host_provenance: bool,
user_provenance: bool,
orcid: str,
fsaccess: StdFsAccess,
run_uuid: Optional[uuid.UUID] = None,
) -> None:
"""Initialize the provenance profile."""
self.fsaccess = fsaccess
self.orcid = orcid
self.research_object = research_object
self.folder = self.research_object.folder
self.document = ProvDocument()
self.host_provenance = host_provenance
self.user_provenance = user_provenance
self.engine_uuid = research_object.engine_uuid # type: str
self.add_to_manifest = self.research_object.add_to_manifest
if self.orcid:
_logger.debug("[provenance] Creator ORCID: %s", self.orcid)
self.full_name = full_name
if self.full_name:
_logger.debug("[provenance] Creator Full name: %s", self.full_name)
self.workflow_run_uuid = run_uuid or uuid.uuid4()
self.workflow_run_uri = self.workflow_run_uuid.urn # type: str
self.generate_prov_doc()
def __str__(self) -> str:
"""Represent this Provenvance profile as a string."""
return "ProvenanceProfile <{}> in <{}>".format(
self.workflow_run_uri,
self.research_object,
)
def generate_prov_doc(self) -> Tuple[str, ProvDocument]:
"""Add basic namespaces."""
def host_provenance(document: ProvDocument) -> None:
"""Record host provenance."""
document.add_namespace(CWLPROV)
document.add_namespace(UUID)
document.add_namespace(FOAF)
hostname = getfqdn()
# won't have a foaf:accountServiceHomepage for unix hosts, but
# we can at least provide hostname
document.agent(
ACCOUNT_UUID,
{
PROV_TYPE: FOAF["OnlineAccount"],
"prov:location": hostname,
CWLPROV["hostname"]: hostname,
},
)
self.cwltool_version = "cwltool %s" % versionstring().split()[-1]
self.document.add_namespace("wfprov",
"http://purl.org/wf4ever/wfprov#")
# document.add_namespace('prov', 'http://www.w3.org/ns/prov#')
self.document.add_namespace("wfdesc",
"http://purl.org/wf4ever/wfdesc#")
# TODO: Make this ontology. For now only has cwlprov:image
self.document.add_namespace("cwlprov", "https://w3id.org/cwl/prov#")
self.document.add_namespace("foaf", "http://xmlns.com/foaf/0.1/")
self.document.add_namespace("schema", "http://schema.org/")
self.document.add_namespace("orcid", "https://orcid.org/")
self.document.add_namespace("id", "urn:uuid:")
# NOTE: Internet draft expired 2004-03-04 (!)
# https://tools.ietf.org/html/draft-thiemann-hash-urn-01
# TODO: Change to nih:sha-256; hashes
# https://tools.ietf.org/html/rfc6920#section-7
self.document.add_namespace("data", "urn:hash::sha1:")
# Also needed for docker images
self.document.add_namespace(SHA256, "nih:sha-256;")
# info only, won't really be used by prov as sub-resources use /
self.document.add_namespace("researchobject",
self.research_object.base_uri)
# annotations
self.metadata_ns = self.document.add_namespace(
"metadata", self.research_object.base_uri + METADATA + "/")
# Pre-register provenance directory so we can refer to its files
self.provenance_ns = self.document.add_namespace(
"provenance",
self.research_object.base_uri + posix_path(PROVENANCE) + "/")
ro_identifier_workflow = self.research_object.base_uri + "workflow/packed.cwl#"
self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow)
ro_identifier_input = (self.research_object.base_uri +
"workflow/primary-job.json#")
self.document.add_namespace("input", ro_identifier_input)
# More info about the account (e.g. username, fullname)
# may or may not have been previously logged by user_provenance()
# .. but we always know cwltool was launched (directly or indirectly)
# by a user account, as cwltool is a command line tool
account = self.document.agent(ACCOUNT_UUID)
if self.orcid or self.full_name:
person = {PROV_TYPE: PROV["Person"], "prov:type": SCHEMA["Person"]}
if self.full_name:
person["prov:label"] = self.full_name
person["foaf:name"] = self.full_name
person["schema:name"] = self.full_name
else:
# TODO: Look up name from ORCID API?
pass
agent = self.document.agent(self.orcid or uuid.uuid4().urn, person)
self.document.actedOnBehalfOf(account, agent)
else:
if self.host_provenance:
host_provenance(self.document)
if self.user_provenance:
self.research_object.user_provenance(self.document)
# The execution of cwltool
wfengine = self.document.agent(
self.engine_uuid,
{
PROV_TYPE: PROV["SoftwareAgent"],
"prov:type": WFPROV["WorkflowEngine"],
"prov:label": self.cwltool_version,
},
)
# FIXME: This datetime will be a bit too delayed, we should
# capture when cwltool.py earliest started?
self.document.wasStartedBy(wfengine, None, account,
datetime.datetime.now())
# define workflow run level activity
self.document.activity(
self.workflow_run_uri,
datetime.datetime.now(),
None,
{
PROV_TYPE: WFPROV["WorkflowRun"],
"prov:label": "Run of workflow/packed.cwl#main",
},
)
# association between SoftwareAgent and WorkflowRun
main_workflow = "wf:main"
self.document.wasAssociatedWith(self.workflow_run_uri,
self.engine_uuid, main_workflow)
self.document.wasStartedBy(self.workflow_run_uri, None,
self.engine_uuid, datetime.datetime.now())
return (self.workflow_run_uri, self.document)
def evaluate(
self,
process: Process,
job: JobsType,
job_order_object: CWLObjectType,
research_obj: "ResearchObject",
) -> None:
"""Evaluate the nature of job."""
if not hasattr(process, "steps"):
# record provenance of independent commandline tool executions
self.prospective_prov(job)
customised_job = copy_job_order(job, job_order_object)
self.used_artefacts(customised_job, self.workflow_run_uri)
research_obj.create_job(customised_job)
elif hasattr(job, "workflow"):
# record provenance of workflow executions
self.prospective_prov(job)
customised_job = copy_job_order(job, job_order_object)
self.used_artefacts(customised_job, self.workflow_run_uri)
def record_process_start(
self,
process: Process,
job: JobsType,
process_run_id: Optional[str] = None) -> Optional[str]:
if not hasattr(process, "steps"):
process_run_id = self.workflow_run_uri
elif not hasattr(job, "workflow"):
# commandline tool execution as part of workflow
name = ""
if isinstance(job, (CommandLineJob, JobBase, WorkflowJob)):
name = job.name
process_name = urllib.parse.quote(name, safe=":/,#")
process_run_id = self.start_process(process_name,
datetime.datetime.now())
return process_run_id
def start_process(
self,
process_name: str,
when: datetime.datetime,
process_run_id: Optional[str] = None,
) -> str:
"""Record the start of each Process."""
if process_run_id is None:
process_run_id = uuid.uuid4().urn
prov_label = "Run of workflow/packed.cwl#main/" + process_name
self.document.activity(
process_run_id,
None,
None,
{
PROV_TYPE: WFPROV["ProcessRun"],
PROV_LABEL: prov_label
},
)
self.document.wasAssociatedWith(process_run_id, self.engine_uuid,
str("wf:main/" + process_name))
self.document.wasStartedBy(process_run_id, None, self.workflow_run_uri,
when, None, None)
return process_run_id
def record_process_end(
self,
process_name: str,
process_run_id: str,
outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None],
when: datetime.datetime,
) -> None:
self.generate_output_prov(outputs, process_run_id, process_name)
self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri,
when)
def declare_file(
self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, str]:
if value["class"] != "File":
raise ValueError("Must have class:File: %s" % value)
# Need to determine file hash aka RO filename
entity = None # type: Optional[ProvEntity]
checksum = None
if "checksum" in value:
csum = cast(str, value["checksum"])
(method, checksum) = csum.split("$", 1)
if method == SHA1 and self.research_object.has_data_file(checksum):
entity = self.document.entity("data:" + checksum)
if not entity and "location" in value:
location = str(value["location"])
# If we made it here, we'll have to add it to the RO
with self.fsaccess.open(location, "rb") as fhandle:
relative_path = self.research_object.add_data_file(fhandle)
# FIXME: This naively relies on add_data_file setting hash as filename
checksum = PurePath(relative_path).name
entity = self.document.entity("data:" + checksum,
{PROV_TYPE: WFPROV["Artifact"]})
if "checksum" not in value:
value["checksum"] = f"{SHA1}${checksum}"
if not entity and "contents" in value:
# Anonymous file, add content as string
entity, checksum = self.declare_string(cast(
str, value["contents"]))
# By here one of them should have worked!
if not entity or not checksum:
raise ValueError(
"class:File but missing checksum/location/content: %r" % value)
# Track filename and extension, this is generally useful only for
# secondaryFiles. Note that multiple uses of a file might thus record
# different names for the same entity, so we'll
# make/track a specialized entity by UUID
file_id = value.setdefault("@id", uuid.uuid4().urn)
# A specialized entity that has just these names
file_entity = self.document.entity(
file_id,
[(PROV_TYPE, WFPROV["Artifact"]), (PROV_TYPE, WF4EVER["File"])],
) # type: ProvEntity
if "basename" in value:
file_entity.add_attributes(
{CWLPROV["basename"]: value["basename"]})
if "nameroot" in value:
file_entity.add_attributes(
{CWLPROV["nameroot"]: value["nameroot"]})
if "nameext" in value:
file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]})
self.document.specializationOf(file_entity, entity)
# Check for secondaries
for sec in cast(MutableSequence[CWLObjectType],
value.get("secondaryFiles", [])):
# TODO: Record these in a specializationOf entity with UUID?
if sec["class"] == "File":
(sec_entity, _, _) = self.declare_file(sec)
elif sec["class"] == "Directory":
sec_entity = self.declare_directory(sec)
else:
raise ValueError(f"Got unexpected secondaryFiles value: {sec}")
# We don't know how/when/where the secondary file was generated,
# but CWL convention is a kind of summary/index derived
# from the original file. As its generally in a different format
# then prov:Quotation is not appropriate.
self.document.derivation(
sec_entity,
file_entity,
other_attributes={PROV["type"]: CWLPROV["SecondaryFile"]},
)
return file_entity, entity, checksum
def declare_directory(self, value: CWLObjectType) -> ProvEntity:
"""Register any nested files/directories."""
# FIXME: Calculate a hash-like identifier for directory
# so we get same value if it's the same filenames/hashes
# in a different location.
# For now, mint a new UUID to identify this directory, but
# attempt to keep it inside the value dictionary
dir_id = cast(str, value.setdefault("@id", uuid.uuid4().urn))
# New annotation file to keep the ORE Folder listing
ore_doc_fn = dir_id.replace("urn:uuid:", "directory-") + ".ttl"
dir_bundle = self.document.bundle(self.metadata_ns[ore_doc_fn])
coll = self.document.entity(
dir_id,
[
(PROV_TYPE, WFPROV["Artifact"]),
(PROV_TYPE, PROV["Collection"]),
(PROV_TYPE, PROV["Dictionary"]),
(PROV_TYPE, RO["Folder"]),
],
)
# ORE description of ro:Folder, saved separately
coll_b = dir_bundle.entity(
dir_id,
[(PROV_TYPE, RO["Folder"]), (PROV_TYPE, ORE["Aggregation"])],
)
self.document.mentionOf(dir_id + "#ore", dir_id, dir_bundle.identifier)
# dir_manifest = dir_bundle.entity(
# dir_bundle.identifier, {PROV["type"]: ORE["ResourceMap"],
# ORE["describes"]: coll_b.identifier})
coll_attribs = [(ORE["isDescribedBy"], dir_bundle.identifier)]
coll_b_attribs = [] # type: List[Tuple[Identifier, ProvEntity]]
# FIXME: .listing might not be populated yet - hopefully
# a later call to this method will sort that
is_empty = True
if "listing" not in value:
get_listing(self.fsaccess, value)
for entry in cast(MutableSequence[CWLObjectType],
value.get("listing", [])):
is_empty = False
# Declare child-artifacts
entity = self.declare_artefact(entry)
self.document.membership(coll, entity)
# Membership relation aka our ORE Proxy
m_id = uuid.uuid4().urn
m_entity = self.document.entity(m_id)
m_b = dir_bundle.entity(m_id)
# PROV-O style Dictionary
# https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition
# ..as prov.py do not currently allow PROV-N extensions
# like hadDictionaryMember(..)
m_entity.add_asserted_type(PROV["KeyEntityPair"])
m_entity.add_attributes({
PROV["pairKey"]: entry["basename"],
PROV["pairEntity"]: entity,
})
# As well as a being a
# http://wf4ever.github.io/ro/2016-01-28/ro/#FolderEntry
m_b.add_asserted_type(RO["FolderEntry"])
m_b.add_asserted_type(ORE["Proxy"])
m_b.add_attributes({
RO["entryName"]: entry["basename"],
ORE["proxyIn"]: coll,
ORE["proxyFor"]: entity,
})
coll_attribs.append((PROV["hadDictionaryMember"], m_entity))
coll_b_attribs.append((ORE["aggregates"], m_b))
coll.add_attributes(coll_attribs)
coll_b.add_attributes(coll_b_attribs)
# Also Save ORE Folder as annotation metadata
ore_doc = ProvDocument()
ore_doc.add_namespace(ORE)
ore_doc.add_namespace(RO)
ore_doc.add_namespace(UUID)
ore_doc.add_bundle(dir_bundle)
ore_doc = ore_doc.flattened()
ore_doc_path = str(PurePosixPath(METADATA, ore_doc_fn))
with self.research_object.write_bag_file(
ore_doc_path) as provenance_file:
ore_doc.serialize(provenance_file,
format="rdf",
rdf_format="turtle")
self.research_object.add_annotation(dir_id, [ore_doc_fn],
ORE["isDescribedBy"].uri)
if is_empty:
# Empty directory
coll.add_asserted_type(PROV["EmptyCollection"])
coll.add_asserted_type(PROV["EmptyDictionary"])
self.research_object.add_uri(coll.identifier.uri)
return coll
def declare_string(self, value: str) -> Tuple[ProvEntity, str]:
"""Save as string in UTF-8."""
byte_s = BytesIO(str(value).encode(ENCODING))
data_file = self.research_object.add_data_file(byte_s,
content_type=TEXT_PLAIN)
checksum = PurePosixPath(data_file).name
# FIXME: Don't naively assume add_data_file uses hash in filename!
data_id = "data:%s" % PurePosixPath(data_file).stem
entity = self.document.entity(data_id, {
PROV_TYPE: WFPROV["Artifact"],
PROV_VALUE: str(value)
}) # type: ProvEntity
return entity, checksum
def declare_artefact(self, value: Optional[CWLOutputType]) -> ProvEntity:
"""Create data artefact entities for all file objects."""
if value is None:
# FIXME: If this can happen in CWL, we'll
# need a better way to represent this in PROV
return self.document.entity(CWLPROV["None"], {PROV_LABEL: "None"})
if isinstance(value, (bool, int, float)):
# Typically used in job documents for flags
# FIXME: Make consistent hash URIs for these
# that somehow include the type
# (so "1" != 1 != "1.0" != true)
entity = self.document.entity(uuid.uuid4().urn,
{PROV_VALUE: value})
self.research_object.add_uri(entity.identifier.uri)
return entity
if isinstance(value, (str, str)):
(entity, _) = self.declare_string(value)
return entity
if isinstance(value, bytes):
# If we got here then we must be in Python 3
byte_s = BytesIO(value)
data_file = self.research_object.add_data_file(byte_s)
# FIXME: Don't naively assume add_data_file uses hash in filename!
data_id = "data:%s" % PurePosixPath(data_file).stem
return self.document.entity(
data_id,
{
PROV_TYPE: WFPROV["Artifact"],
PROV_VALUE: str(value)
},
)
if isinstance(value, MutableMapping):
if "@id" in value:
# Already processed this value, but it might not be in this PROV
entities = self.document.get_record(value["@id"])
if entities:
return entities[0]
# else, unknown in PROV, re-add below as if it's fresh
# Base case - we found a File we need to update
if value.get("class") == "File":
(entity, _, _) = self.declare_file(value)
value["@id"] = entity.identifier.uri
return entity
if value.get("class") == "Directory":
entity = self.declare_directory(value)
value["@id"] = entity.identifier.uri
return entity
coll_id = value.setdefault("@id", uuid.uuid4().urn)
# some other kind of dictionary?
# TODO: also Save as JSON
coll = self.document.entity(
coll_id,
[
(PROV_TYPE, WFPROV["Artifact"]),
(PROV_TYPE, PROV["Collection"]),
(PROV_TYPE, PROV["Dictionary"]),
],
)
if value.get("class"):
_logger.warning("Unknown data class %s.", value["class"])
# FIXME: The class might be "http://example.com/somethingelse"
coll.add_asserted_type(CWLPROV[value["class"]])
# Let's iterate and recurse
coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]]
for (key, val) in value.items():
v_ent = self.declare_artefact(val)
self.document.membership(coll, v_ent)
m_entity = self.document.entity(uuid.uuid4().urn)
# Note: only support PROV-O style dictionary
# https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition
# as prov.py do not easily allow PROV-N extensions
m_entity.add_asserted_type(PROV["KeyEntityPair"])
m_entity.add_attributes({
PROV["pairKey"]: str(key),
PROV["pairEntity"]: v_ent
})
coll_attribs.append((PROV["hadDictionaryMember"], m_entity))
coll.add_attributes(coll_attribs)
self.research_object.add_uri(coll.identifier.uri)
return coll
# some other kind of Collection?
# TODO: also save as JSON
try:
members = []
for each_input_obj in iter(value):
# Recurse and register any nested objects
e = self.declare_artefact(each_input_obj)
members.append(e)
# If we reached this, then we were allowed to iterate
coll = self.document.entity(
uuid.uuid4().urn,
[
(PROV_TYPE, WFPROV["Artifact"]),
(PROV_TYPE, PROV["Collection"]),
],
)
if not members:
coll.add_asserted_type(PROV["EmptyCollection"])
else:
for member in members:
# FIXME: This won't preserve order, for that
# we would need to use PROV.Dictionary
# with numeric keys
self.document.membership(coll, member)
self.research_object.add_uri(coll.identifier.uri)
# FIXME: list value does not support adding "@id"
return coll
except TypeError:
_logger.warning("Unrecognized type %s of %r", type(value), value)
# Let's just fall back to Python repr()
entity = self.document.entity(uuid.uuid4().urn,
{PROV_LABEL: repr(value)})
self.research_object.add_uri(entity.identifier.uri)
return entity
def used_artefacts(
self,
job_order: Union[CWLObjectType, List[CWLObjectType]],
process_run_id: str,
name: Optional[str] = None,
) -> None:
"""Add used() for each data artefact."""
if isinstance(job_order, list):
for entry in job_order:
self.used_artefacts(entry, process_run_id, name)
else:
# FIXME: Use workflow name in packed.cwl, "main" is wrong for nested workflows
base = "main"
if name is not None:
base += "/" + name
for key, value in job_order.items():
prov_role = self.wf_ns[f"{base}/{key}"]
try:
entity = self.declare_artefact(value)
self.document.used(
process_run_id,
entity,
datetime.datetime.now(),
None,
{"prov:role": prov_role},
)
except OSError:
pass
def generate_output_prov(
self,
final_output: Union[CWLObjectType, MutableSequence[CWLObjectType],
None],
process_run_id: Optional[str],
name: Optional[str],
) -> None:
"""Call wasGeneratedBy() for each output,copy the files into the RO."""
if isinstance(final_output, MutableSequence):
for entry in final_output:
self.generate_output_prov(entry, process_run_id, name)
elif final_output is not None:
# Timestamp should be created at the earliest
timestamp = datetime.datetime.now()
# For each output, find/register the corresponding
# entity (UUID) and document it as generated in
# a role corresponding to the output
for output, value in final_output.items():
entity = self.declare_artefact(value)
if name is not None:
name = urllib.parse.quote(str(name), safe=":/,#")
# FIXME: Probably not "main" in nested workflows
role = self.wf_ns[f"main/{name}/{output}"]
else:
role = self.wf_ns["main/%s" % output]
if not process_run_id:
process_run_id = self.workflow_run_uri
self.document.wasGeneratedBy(entity, process_run_id, timestamp,
None, {"prov:role": role})
def prospective_prov(self, job: JobsType) -> None:
"""Create prospective prov recording as wfdesc prov:Plan."""
if not isinstance(job, WorkflowJob):
# direct command line tool execution
self.document.entity(
"wf:main",
{
PROV_TYPE: WFDESC["Process"],
"prov:type": PROV["Plan"],
"prov:label": "Prospective provenance",
},
)
return
self.document.entity(
"wf:main",
{
PROV_TYPE: WFDESC["Workflow"],
"prov:type": PROV["Plan"],
"prov:label": "Prospective provenance",
},
)
for step in job.steps:
stepnametemp = "wf:main/" + str(step.name)[5:]
stepname = urllib.parse.quote(stepnametemp, safe=":/,#")
provstep = self.document.entity(
stepname,
{
PROV_TYPE: WFDESC["Process"],
"prov:type": PROV["Plan"]
},
)
self.document.entity(
"wf:main",
{
"wfdesc:hasSubProcess": provstep,
"prov:label": "Prospective provenance",
},
)
# TODO: Declare roles/parameters as well
def activity_has_provenance(self, activity, prov_ids):
# type: (str, List[Identifier]) -> None
"""Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files."""
# NOTE: The below will only work if the corresponding metadata/provenance arcp URI
# is a pre-registered namespace in the PROV Document
attribs = [(PROV["has_provenance"], prov_id) for prov_id in prov_ids]
self.document.activity(activity, other_attributes=attribs)
# Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention
# as prov:mentionOf() is only for entities, not activities
uris = [i.uri for i in prov_ids]
self.research_object.add_annotation(activity, uris,
PROV["has_provenance"].uri)
def finalize_prov_profile(self, name):
# type: (Optional[str]) -> List[Identifier]
"""Transfer the provenance related files to the RO."""
# NOTE: Relative posix path
if name is None:
# main workflow, fixed filenames
filename = "primary.cwlprov"
else:
# ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json
wf_name = urllib.parse.quote(str(name), safe="").replace("%", "_")
# Note that the above could cause overlaps for similarly named
# workflows, but that's OK as we'll also include run uuid
# which also covers thhe case of this step being run in
# multiple places or iterations
filename = f"{wf_name}.{self.workflow_run_uuid}.cwlprov"
basename = str(PurePosixPath(PROVENANCE) / filename)
# TODO: Also support other profiles than CWLProv, e.g. ProvOne
# list of prov identifiers of provenance files
prov_ids = []
# https://www.w3.org/TR/prov-xml/
with self.research_object.write_bag_file(basename +
".xml") as provenance_file:
self.document.serialize(provenance_file, format="xml", indent=4)
prov_ids.append(self.provenance_ns[filename + ".xml"])
# https://www.w3.org/TR/prov-n/
with self.research_object.write_bag_file(basename +
".provn") as provenance_file:
self.document.serialize(provenance_file, format="provn", indent=2)
prov_ids.append(self.provenance_ns[filename + ".provn"])
# https://www.w3.org/Submission/prov-json/
with self.research_object.write_bag_file(basename +
".json") as provenance_file:
self.document.serialize(provenance_file, format="json", indent=2)
prov_ids.append(self.provenance_ns[filename + ".json"])
# "rdf" aka https://www.w3.org/TR/prov-o/
# which can be serialized to ttl/nt/jsonld (and more!)
# https://www.w3.org/TR/turtle/
with self.research_object.write_bag_file(basename +
".ttl") as provenance_file:
self.document.serialize(provenance_file,
format="rdf",
rdf_format="turtle")
prov_ids.append(self.provenance_ns[filename + ".ttl"])
# https://www.w3.org/TR/n-triples/
with self.research_object.write_bag_file(basename +
".nt") as provenance_file:
self.document.serialize(provenance_file,
format="rdf",
rdf_format="ntriples")
prov_ids.append(self.provenance_ns[filename + ".nt"])
# https://www.w3.org/TR/json-ld/
# TODO: Use a nice JSON-LD context
# see also https://eprints.soton.ac.uk/395985/
# 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :(
with self.research_object.write_bag_file(basename +
".jsonld") as provenance_file:
self.document.serialize(provenance_file,
format="rdf",
rdf_format="json-ld")
prov_ids.append(self.provenance_ns[filename + ".jsonld"])
_logger.debug("[provenance] added provenance: %s", prov_ids)
return prov_ids
def get_provenance_history(self, driver, uuid, depth=None):
prov_doc = ProvDocument()
#prov_doc.
#NOTE!! There is a bug with the JSON serializer. I can't add the prov prefix using this mechanism
prov_doc.add_namespace('ex', 'http://example.org/')
prov_doc.add_namespace('hubmap', 'https://hubmapconsortium.org/')
#prov_doc.add_namespace('dct', 'http://purl.org/dc/terms/')
#prov_doc.add_namespace('foaf','http://xmlns.com/foaf/0.1/')
relation_list = []
with driver.session() as session:
try:
# max_level_str is the string used to put a limit on the number of levels to traverse
max_level_str = ''
if depth is not None and len(str(depth)) > 0:
max_level_str = """maxLevel: {depth},""".format(
depth=depth)
"""
Basically this Cypher query returns a collection of nodes and relationships. The relationships include ACTIVITY_INPUT, ACTIVITY_OUTPUT and
HAS_METADATA. First, we build a dictionary of the nodes using uuid as a key. Next, we loop through the relationships looking for HAS_METADATA
relationships. The HAS_METADATA relationships connect the Entity nodes with their metadata. The data from the Metadata node
becomes the 'metadata' attribute for the Entity node.
"""
"""Possible replacement:
THIS WORKS...NEEDS LOTS of COMMENTS!!
MATCH (entity_metadata)<-[r1:HAS_METADATA]-(e)<-[r2:ACTIVITY_OUTPUT]-(a:Activity)-[r3:HAS_METADATA]->(activity_metadata)
WHERE e.hubmap_identifier = 'TEST0010-LK-1-1'
WITH [e,a, entity_metadata, activity_metadata] AS entities, COLLECT(r1) + COLLECT(r2) + COLLECT(r3) AS relationships
WITH [node in entities | node {.*, label:labels(node)}] AS nodes, [rel in relationships | rel { .*, fromNode: { label:labels(startNode(rel))[0], uuid:startNode(rel).uuid } , toNode: { label:labels(endNode(rel))[0], uuid:endNode(rel).uuid }, rel_data: { type: type(rel) } } ] as rels
RETURN nodes, rels
UNION OPTIONAL MATCH (activity_metadata)<-[r1:HAS_METADATA]-(a:Activity)<-[r2:ACTIVITY_INPUT|:ACTIVITY_OUTPUT*]-(parent)-[r3:HAS_METADATA]->(parent_metadata),
(e)<-[r4:ACTIVITY_OUTPUT]-(a:Activity)
WHERE e.hubmap_identifier = 'TEST0010-LK-1-1'
WITH [parent,parent_metadata, a, activity_metadata] AS nodes, [rel in COLLECT(r1) + COLLECT(r3) + COLLECT(r4)+COLLECT(apoc.convert.toRelationship(r2)) | rel { .*, fromNode: { label:labels(startNode(rel))[0], uuid:startNode(rel).uuid } , toNode: { label:labels(endNode(rel))[0], uuid:endNode(rel).uuid }, rel_data: { type: type(rel) } } ] as rels
RETURN DISTINCT nodes, rels
uuid for TEST0010-LK-1-1 for testing: eda3916db4695d834eb6c51a893d06f1
"""
stmt = """MATCH (n:Entity {{ uuid: '{uuid}' }})
CALL apoc.path.subgraphAll(n, {{ {max_level_str} relationshipFilter:'<ACTIVITY_INPUT|<ACTIVITY_OUTPUT|HAS_METADATA>' }}) YIELD nodes, relationships
WITH [node in nodes | node {{ .*, label:labels(node)[0] }} ] as nodes,
[rel in relationships | rel {{ .*, fromNode: {{ label:labels(startNode(rel))[0], uuid:startNode(rel).uuid }} , toNode: {{ label:labels(endNode(rel))[0], uuid:endNode(rel).uuid }}, rel_data: {{ type: type(rel) }} }} ] as rels
WITH {{ nodes:nodes, relationships:rels }} as json
RETURN json""".format(uuid=uuid, max_level_str=max_level_str)
result = session.run(stmt)
#there should only be one record
for jsonData in result:
try:
record = dict(jsonData)['json']
if 'relationships' not in record:
raise LookupError(
'Error, unable to find relationships for uuid:'
+ uuid)
if 'nodes' not in record:
raise LookupError(
'Error, unable to find nodes for uuid:' + uuid)
node_dict = {}
# pack the nodes into a dictionary using the uuid as a key
for node_record in record['nodes']:
node_dict[node_record['uuid']] = node_record
# TODO: clean up nodes
# remove nodes that lack metadata
# need to devise a methodology for this
# try preprocessing the record['relationships'] here:
# make a copy of the node_dict called unreferenced_node_dict
# loop through the relationships and find all the has_metadata relationships
# for each node pair in the has_metadata relationship, delete it from the unreferenced_node_dict
# once the loop is finished, continue as before
# add some logic when generating the wasGenerated and used relationships. If either node is in the
# unreferenced_node_dict, then ignore the relationship
# now, connect the nodes
for rel_record in record['relationships']:
from_uuid = rel_record['fromNode']['uuid']
to_uuid = rel_record['toNode']['uuid']
from_node = node_dict[from_uuid]
to_node = node_dict[to_uuid]
if rel_record['rel_data'][
'type'] == HubmapConst.HAS_METADATA_REL:
# assign the metadata node as the metadata attribute
# just extract the provenance information from the metadata node
entity_timestamp_json = Provenance.get_json_timestamp(
int(to_node[
HubmapConst.
PROVENANCE_CREATE_TIMESTAMP_ATTRIBUTE])
)
provenance_data = {
ProvConst.PROV_GENERATED_TIME_ATTRIBUTE:
entity_timestamp_json
}
type_code = None
isEntity = True
if HubmapConst.ENTITY_TYPE_ATTRIBUTE in from_node:
type_code = from_node[
HubmapConst.ENTITY_TYPE_ATTRIBUTE]
elif HubmapConst.ACTIVITY_TYPE_ATTRIBUTE in from_node:
type_code = from_node[
HubmapConst.ACTIVITY_TYPE_ATTRIBUTE]
isEntity = False
label_text = None
if HubmapConst.LAB_IDENTIFIER_ATTRIBUTE in from_node:
label_text = from_node[
HubmapConst.LAB_IDENTIFIER_ATTRIBUTE]
else:
label_text = from_node[
HubmapConst.UUID_ATTRIBUTE]
# build metadata attribute from the Metadata node
metadata_attribute = {}
for attribute_key in to_node:
if attribute_key not in self.metadata_ignore_attributes:
if attribute_key in self.known_attribute_map:
# special case: timestamps
if attribute_key == HubmapConst.PROVENANCE_MODIFIED_TIMESTAMP_ATTRIBUTE:
provenance_data[
self.known_attribute_map[
attribute_key]] = Provenance.get_json_timestamp(
int(to_node[
attribute_key])
)
else: #add any extraneous data to the metadata attribute
metadata_attribute[
attribute_key] = to_node[
attribute_key]
# Need to add the agent and organization here, plus the appropriate relationships (between the entity and the agent plus orgainzation)
agent_record = self.get_agent_record(to_node)
agent_unique_id = str(agent_record[
ProvConst.HUBMAP_PROV_USER_EMAIL]).replace(
'@', '-')
agent_unique_id = str(agent_unique_id).replace(
'.', '-')
if ProvConst.HUBMAP_PROV_USER_UUID in agent_record:
agent_unique_id = agent_record[
ProvConst.HUBMAP_PROV_USER_UUID]
agent_uri = Provenance.build_uri(
'hubmap', 'agent', agent_unique_id)
organization_record = self.get_organization_record(
to_node)
organization_uri = Provenance.build_uri(
'hubmap', 'organization',
organization_record[
ProvConst.HUBMAP_PROV_GROUP_UUID])
doc_agent = None
doc_org = None
get_agent = prov_doc.get_record(agent_uri)
# only add this once
if len(get_agent) == 0:
doc_agent = prov_doc.agent(
agent_uri, agent_record)
else:
doc_agent = get_agent[0]
get_org = prov_doc.get_record(organization_uri)
# only add this once
if len(get_org) == 0:
doc_org = prov_doc.agent(
organization_uri, organization_record)
else:
doc_org = get_org[0]
other_attributes = {
ProvConst.PROV_LABEL_ATTRIBUTE:
label_text,
ProvConst.PROV_TYPE_ATTRIBUTE:
type_code,
ProvConst.HUBMAP_DOI_ATTRIBUTE:
from_node[HubmapConst.DOI_ATTRIBUTE],
ProvConst.HUBMAP_DISPLAY_DOI_ATTRIBUTE:
from_node[
HubmapConst.DISPLAY_DOI_ATTRIBUTE],
ProvConst.HUBMAP_DISPLAY_IDENTIFIER_ATTRIBUTE:
label_text,
ProvConst.HUBMAP_UUID_ATTRIBUTE:
from_node[HubmapConst.UUID_ATTRIBUTE]
}
# only add metadata if it contains data
if len(metadata_attribute) > 0:
other_attributes[
ProvConst.
HUBMAP_METADATA_ATTRIBUTE] = json.dumps(
metadata_attribute)
# add the provenance data to the other_attributes
other_attributes.update(provenance_data)
if isEntity == True:
prov_doc.entity(
Provenance.build_uri(
'hubmap', 'entities',
from_node['uuid']),
other_attributes)
else:
activity_timestamp_json = Provenance.get_json_timestamp(
int(to_node[
HubmapConst.
PROVENANCE_CREATE_TIMESTAMP_ATTRIBUTE]
))
doc_activity = prov_doc.activity(
Provenance.build_uri(
'hubmap', 'activities',
from_node['uuid']),
activity_timestamp_json,
activity_timestamp_json,
other_attributes)
prov_doc.actedOnBehalfOf(
doc_agent, doc_org, doc_activity)
elif rel_record['rel_data']['type'] in [
HubmapConst.ACTIVITY_OUTPUT_REL,
HubmapConst.ACTIVITY_INPUT_REL
]:
to_node_uri = None
from_node_uri = None
if HubmapConst.ENTITY_TYPE_ATTRIBUTE in to_node:
to_node_uri = Provenance.build_uri(
'hubmap', 'entities', to_node['uuid'])
else:
to_node_uri = Provenance.build_uri(
'hubmap', 'activities',
to_node['uuid'])
if HubmapConst.ENTITY_TYPE_ATTRIBUTE in from_node:
from_node_uri = Provenance.build_uri(
'hubmap', 'entities',
from_node['uuid'])
else:
from_node_uri = Provenance.build_uri(
'hubmap', 'activities',
from_node['uuid'])
if rel_record['rel_data'][
'type'] == 'ACTIVITY_OUTPUT':
#prov_doc.wasGeneratedBy(entity, activity, time, identifier, other_attributes)
prov_doc.wasGeneratedBy(
to_node_uri, from_node_uri)
if rel_record['rel_data'][
'type'] == 'ACTIVITY_INPUT':
#prov_doc.used(activity, entity, time, identifier, other_attributes)
prov_doc.used(to_node_uri, from_node_uri)
# for now, simply create a "relation" where the fromNode's uuid is connected to a toNode's uuid via a relationship:
# ex: {'fromNodeUUID': '42e10053358328c9079f1c8181287b6d', 'relationship': 'ACTIVITY_OUTPUT', 'toNodeUUID': '398400024fda58e293cdb435db3c777e'}
rel_data_record = {
'fromNodeUUID': from_node['uuid'],
'relationship':
rel_record['rel_data']['type'],
'toNodeUUID': to_node['uuid']
}
relation_list.append(rel_data_record)
return_data = {
'nodes': node_dict,
'relations': relation_list
}
except Exception as e:
raise e
# there is a bug in the JSON serializer. So manually insert the prov prefix
output_doc = prov_doc.serialize(indent=2)
output_doc = output_doc.replace(
'"prefix": {',
'"prefix": {\n "prov" : "http://www.w3.org/ns/prov#", ')
#output_doc = prov_doc.serialize(format='rdf', rdf_format='trig')
#output_doc = prov_doc.serialize(format='provn')
return output_doc
except ConnectionError as ce:
print('A connection error occurred: ', str(ce.args[0]))
raise ce
except ValueError as ve:
print('A value error occurred: ', ve.value)
raise ve
except Exception as e:
print('An exception occurred in get_provenance_history: ' +
str(e))
traceback.print_exc()
