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import time
from com.googlecode.fascinator.api.storage import StorageException
from com.googlecode.fascinator.common import JsonSimple
from com.googlecode.fascinator.common.storage import StorageUtils
from java.util import HashSet, HashMap
from org.apache.commons.io import IOUtils
class IndexData:
def __activate__(self, context):
# Prepare variables
self.index = context["fields"]
self.object = context["object"]
self.payload = context["payload"]
self.params = context["params"]
self.utils = context["pyUtils"]
self.config = context["jsonConfig"]
self.log = context["log"]
self.last_modified = time.strftime("%Y-%m-%dT%H:%M:%SZ", time.gmtime())
self.log.debug("Indexing Metadata Record '{}' '{}'", self.object.getId(), self.payload.getId())
# Common data
self.__newDoc()
self.packagePid = None
pidList = self.object.getPayloadIdList()
for pid in pidList:
if pid.endswith(".tfpackage"):
self.packagePid = pid
# Real metadata
if self.itemType == "object":
self.__basicData()
self.__metadata()
# Some of the above steps may request some
# messages be sent, particularly workflows
self.__messages()
# Make sure security comes after workflows
self.__security()
def __newDoc(self):
self.oid = self.object.getId()
self.pid = self.payload.getId()
metadataPid = self.params.getProperty("metaPid", "DC")
self.utils.add(self.index, "storage_id", self.oid)
if self.pid == metadataPid:
self.itemType = "object"
else:
self.oid += "/" + self.pid
self.itemType = "datastream"
self.utils.add(self.index, "identifier", self.pid)
self.utils.add(self.index, "id", self.oid)
self.utils.add(self.index, "item_type", self.itemType)
self.utils.add(self.index, "last_modified", self.last_modified)
self.utils.add(self.index, "harvest_config", self.params.getProperty("jsonConfigOid"))
self.utils.add(self.index, "harvest_rules", self.params.getProperty("rulesOid"))
self.item_security = []
self.owner = self.params.getProperty("owner", "guest")
def __basicData(self):
self.utils.add(self.index, "repository_name", self.params["repository.name"])
self.utils.add(self.index, "repository_type", self.params["repository.type"])
# VITAL integration
vitalPid = self.params["vitalPid"]
if vitalPid is not None:
self.utils.add(self.index, "vitalPid", vitalPid)
# Persistent Identifiers
pidProperty = self.config.getString(None, ["curation", "pidProperty"])
if pidProperty is None:
self.log.error("No configuration found for persistent IDs!")
else:
pid = self.params[pidProperty]
if pid is not None:
self.utils.add(self.index, "known_ids", pid)
self.utils.add(self.index, "pidProperty", pid)
self.utils.add(self.index, "oai_identifier", pid)
self.utils.add(self.index, "oai_set", "default")
# Publication
published = self.params["published"]
if published is not None:
self.utils.add(self.index, "published", "true")
def __security(self):
# Security
roles = self.utils.getRolesWithAccess(self.oid)
if roles is not None:
# For every role currently with access
for role in roles:
# Should show up, but during debugging we got a few
if role != "":
if role in self.item_security:
# They still have access
self.utils.add(self.index, "security_filter", role)
else:
# Their access has been revoked
self.__revokeRoleAccess(role)
# Now for every role that the new step allows access
for role in self.item_security:
if role not in roles:
# Grant access if new
self.__grantRoleAccess(role)
self.utils.add(self.index, "security_filter", role)
# No existing security
else:
if self.item_security is None:
# Guest access if none provided so far
self.__grantRoleAccess("guest")
self.utils.add(self.index, "security_filter", role)
else:
# Otherwise use workflow security
for role in self.item_security:
# Grant access if new
self.__grantRoleAccess(role)
self.utils.add(self.index, "security_filter", role)
users = self.utils.getUsersWithAccess(self.oid)
if users is not None:
# For every role currently with access
for user in users:
self.utils.add(self.index, "security_exception", user)
# Ownership
if self.owner is None:
self.utils.add(self.index, "owner", "system")
else:
self.utils.add(self.index, "owner", self.owner)
def __indexList(self, name, values):
# convert to set so no duplicate values
for value in HashSet(values):
self.utils.add(self.index, name, value)
def __grantRoleAccess(self, newRole):
schema = self.utils.getAccessSchema("derby");
schema.setRecordId(self.oid)
schema.set("role", newRole)
self.utils.setAccessSchema(schema, "derby")
def __grantUserAccess(self, newUser):
schema = self.utils.getAccessSchema("derby");
schema.setRecordId(self.oid)
schema.set("user", newUser)
self.utils.setAccessSchema(schema, "derby")
def __revokeRoleAccess(self, oldRole):
schema = self.utils.getAccessSchema("derby");
schema.setRecordId(self.oid)
schema.set("role", oldRole)
self.utils.removeAccessSchema(schema, "derby")
def __revokeUserAccess(self, oldUser):
schema = self.utils.getAccessSchema("derby");
schema.setRecordId(self.oid)
schema.set("user", oldUser)
self.utils.removeAccessSchema(schema, "derby")
def __metadata(self):
self.title = None
self.dcType = None
self.descriptionList = []
self.creatorList = []
self.creationDate = []
self.contributorList = []
self.approverList = []
self.formatList = ["application/x-fascinator-package"]
self.fulltext = []
self.relationDict = {}
self.customFields = {}
self.creatorFullNameMap = HashMap()
self.grantNumberList = []
self.arrayBucket = HashMap()
self.compFields = ["dc:coverage.vivo:DateTimeInterval", "locrel:prc.foaf:Person"]
self.compFieldsConfig = {"dc:coverage.vivo:DateTimeInterval":{"delim":" to ","start":"start","end":"end"},"locrel:prc.foaf:Person":{"delim":", ","start":"familyName","end":"givenName"} }
self.reportingFieldPrefix = "reporting_"
self.embargoedDate = None
# Try our data sources, order matters
self.__workflow()
# Some defaults if the above failed
if self.title is None:
self.title = "New Dataset"
if self.formatList == []:
source = self.object.getPayload(self.packagePid)
self.formatList.append(source.getContentType())
# Index our metadata finally
self.utils.add(self.index, "dc_title", self.title)
if self.dcType is not None:
self.utils.add(self.index, "dc_type", self.dcType)
self.__indexList("dc_creator", self.creatorList) #no dc_author in schema.xml, need to check
self.__indexList("dc_contributor", self.contributorList)
self.__indexList("dc_description", self.descriptionList)
self.__indexList("dc_format", self.formatList)
self.__indexList("dc_date", self.creationDate)
self.__indexList("full_text", self.fulltext)
for key in self.customFields:
self.__indexList(key, self.customFields[key])
for key in self.relationDict:
self.__indexList(key, self.relationDict[key])
if self.arrayBucket.size() > 0:
for arrFldName in self.arrayBucket.keySet():
if arrFldName.endswith("Person") or arrFldName.replace(self.reportingFieldPrefix, "") in self.compFields:
self.__indexList(arrFldName, self.arrayBucket.get(arrFldName).values())
else:
self.__indexList(arrFldName, self.arrayBucket.get(arrFldName))
if self.embargoedDate is not None:
self.utils.add(self.index, "date_embargoed", self.embargoedDate+"T00:00:00Z")
def __workflow(self):
# Workflow data
WORKFLOW_ID = "dataset"
wfChanged = False
workflow_security = []
self.message_list = None
stages = self.config.getJsonSimpleList(["stages"])
if self.owner == "guest":
pageTitle = "Submission Request"
displayType = "submission-request"
initialStep = 0
else:
pageTitle = "Metadata Record"
displayType = "package-dataset"
initialStep = 1
try:
wfMeta = self.__getJsonPayload("workflow.metadata")
wfMeta.getJsonObject().put("pageTitle", pageTitle)
# Are we indexing because of a workflow progression?
targetStep = wfMeta.getString(None, ["targetStep"])
if targetStep is not None and targetStep != wfMeta.getString(None, ["step"]):
wfChanged = True
# Step change
wfMeta.getJsonObject().put("step", targetStep)
wfMeta.getJsonObject().remove("targetStep")
# This must be a re-index then
else:
targetStep = wfMeta.getString(None, ["step"])
# Security change
for stage in stages:
if stage.getString(None, ["name"]) == targetStep:
wfMeta.getJsonObject().put("label", stage.getString(None, ["label"]))
self.item_security = stage.getStringList(["visibility"])
workflow_security = stage.getStringList(["security"])
if wfChanged == True:
self.message_list = stage.getStringList(["message"])
except StorageException:
# No workflow payload, time to create
initialStage = stages.get(initialStep).getString(None, ["name"])
wfChanged = True
wfMeta = JsonSimple()
wfMetaObj = wfMeta.getJsonObject()
wfMetaObj.put("id", WORKFLOW_ID)
wfMetaObj.put("step", initialStage)
wfMetaObj.put("pageTitle", pageTitle)
stages = self.config.getJsonSimpleList(["stages"])
for stage in stages:
if stage.getString(None, ["name"]) == initialStage:
wfMetaObj.put("label", stage.getString(None, ["label"]))
self.item_security = stage.getStringList(["visibility"])
workflow_security = stage.getStringList(["security"])
self.message_list = stage.getStringList(["message"])
# Has the workflow metadata changed?
if wfChanged == True:
inStream = IOUtils.toInputStream(wfMeta.toString(True), "UTF-8")
try:
StorageUtils.createOrUpdatePayload(self.object, "workflow.metadata", inStream)
except StorageException:
print " ERROR updating dataset payload"
# Form processing
coreFields = ["title", "description", "manifest", "metaList", "relationships", "responses"]
formData = wfMeta.getObject(["formData"])
if formData is not None:
formData = JsonSimple(formData)
# Core fields
description = formData.getStringList(["description"])
if description:
self.descriptionList = description
# Non-core fields
data = formData.getJsonObject()
for field in data.keySet():
if field not in coreFields:
self.customFields[field] = formData.getStringList([field])
# Manifest processing (formData not present in wfMeta)
manifest = self.__getJsonPayload(self.packagePid)
formTitles = manifest.getStringList(["title"])
if formTitles:
for formTitle in formTitles:
if self.title is None:
self.title = formTitle
self.descriptionList = [manifest.getString("", ["description"])]
#Used to make sure we have a created date
createdDateFlag = False
formData = manifest.getJsonObject()
for field in formData.keySet():
if field not in coreFields:
value = formData.get(field)
if value is not None and value.strip() != "":
self.utils.add(self.index, field, value)
# We want to sort by date of creation, so it
# needs to be indexed as a date (ie. 'date_*')
if field == "dc:created":
parsedTime = time.strptime(value, "%Y-%m-%d")
solrTime = time.strftime("%Y-%m-%dT%H:%M:%SZ", parsedTime)
self.utils.add(self.index, "date_created", solrTime)
self.log.debug("Set created date to :%s" % solrTime)
createdDateFlag = True
elif field == "redbox:embargo.dc:date":
self.embargoedDate = value
# try to extract some common fields for faceting
if field.startswith("dc:") and \
not (field.endswith(".dc:identifier.rdf:PlainLiteral") \
or field.endswith(".dc:identifier") \
or field.endswith(".rdf:resource")):
# index dublin core fields for faceting
basicField = field.replace("dc:", "dc_")
dot = field.find(".")
if dot > 0:
facetField = basicField[:dot]
else:
facetField = basicField
#print "Indexing DC field '%s':'%s'" % (field, facetField)
if facetField == "dc_title":
if self.title is None:
self.title = value
elif facetField == "dc_type":
if self.dcType is None:
self.dcType = value
elif facetField == "dc_creator":
if basicField.endswith("foaf_name"):
self.utils.add(self.index, "dc_creator", value)
else:
self.utils.add(self.index, facetField, value)
# index keywords for lookup
if field.startswith("dc:subject.vivo:keyword."):
self.utils.add(self.index, "keywords", value)
# check if this is an array field
fnameparts = field.split(":")
if fnameparts is not None and len(fnameparts) >= 3:
if field.startswith("bibo") or field.startswith("skos"):
arrParts = fnameparts[1].split(".")
else:
arrParts = fnameparts[2].split(".")
# we're not interested in: Relationship, Type and some redbox:origin
if arrParts is not None and len(arrParts) >= 2 and field.find(":Relationship.") == -1 and field.find("dc:type") == -1 and field.find("redbox:origin") == -1 and arrParts[1].isdigit():
# we've got an array field
fldPart = ":%s" % arrParts[0]
prefixEndIdx = field.find(fldPart) + len(fldPart)
suffixStartIdx = prefixEndIdx+len(arrParts[1])+1
arrFldName = self.reportingFieldPrefix + field[:prefixEndIdx] + field[suffixStartIdx:]
if field.endswith("Name"):
arrFldName = self.reportingFieldPrefix + field[:prefixEndIdx]
self.log.debug("Array Field name is:%s from: %s, with value:%s" % (arrFldName, field, value))
if field.endswith("Name"):
fullFieldMap = self.arrayBucket.get(arrFldName)
if fullFieldMap is None:
fullFieldMap = HashMap()
self.arrayBucket.put(arrFldName, fullFieldMap)
idx = arrParts[1]
fullField = fullFieldMap.get(idx)
if (fullField is None):
fullField = ""
if (field.endswith("givenName")):
fullField = "%s, %s" % (fullField, value)
if (field.endswith("familyName")):
fullField = "%s%s" % (value, fullField)
self.log.debug("fullname now is :%s" % fullField)
fullFieldMap.put(idx, fullField)
else:
fieldlist = self.arrayBucket.get(arrFldName)
if fieldlist is None:
fieldlist = []
self.arrayBucket.put(arrFldName, fieldlist)
fieldlist.append(value)
for compfield in self.compFields:
if field.startswith(compfield):
arrFldName = self.reportingFieldPrefix +compfield
fullFieldMap = self.arrayBucket.get(arrFldName)
if fullFieldMap is None:
fullFieldMap = HashMap()
self.arrayBucket.put(arrFldName, fullFieldMap)
fullField = fullFieldMap.get("1")
if fullField is None:
fullField = ""
if field.endswith(self.compFieldsConfig[compfield]["end"]):
fullField = "%s%s%s" % (fullField, self.compFieldsConfig[compfield]["delim"] ,value)
if field.endswith(self.compFieldsConfig[compfield]["start"]):
fullField = "%s%s" % (value, fullField)
self.log.debug("full field now is :%s" % fullField)
fullFieldMap.put("1", fullField)
self.utils.add(self.index, "display_type", displayType)
# Make sure we have a creation date
if not createdDateFlag:
self.utils.add(self.index, "date_created", self.last_modified)
self.log.debug("Forced creation date to %s because it was not explicitly set." % self.last_modified)
# Workflow processing
wfStep = wfMeta.getString(None, ["step"])
self.utils.add(self.index, "workflow_id", wfMeta.getString(None, ["id"]))
self.utils.add(self.index, "workflow_step", wfStep)
self.utils.add(self.index, "workflow_step_label", wfMeta.getString(None, ["label"]))
for group in workflow_security:
self.utils.add(self.index, "workflow_security", group)
if self.owner is not None:
self.utils.add(self.index, "workflow_security", self.owner)
# set OAI-PMH status to deleted
if wfStep == "retired":
self.utils.add(self.index, "oai_deleted", "true")
def __messages(self):
if self.message_list is not None and len(self.message_list) > 0:
msg = JsonSimple()
msg.getJsonObject().put("oid", self.oid)
message = msg.toString()
for target in self.message_list:
self.utils.sendMessage(target, message)
def __getJsonPayload(self, pid):
payload = self.object.getPayload(pid)
json = self.utils.getJsonObject(payload.open())
payload.close()
return json
