def updateRelationships(self, relationship,pid,identifier):
oid = self.findOidByIdentifier(relationship.get("identifier"))
self.writer.println(oid)
digitalObject = StorageUtils.getDigitalObject(self.storage, oid)
metadataJsonPayload = digitalObject.getPayload("metadata.json")
metadataJsonInstream = metadataJsonPayload.open()
metadataJson = JsonSimple(metadataJsonInstream)
metadataJsonPayload.close()
relationships = metadataJson.getArray("relationships")
found = False
if relationships is None:
relationships = JSONArray()
metadataJson.getJsonObject().put("relationships",relationships)
for relationship1 in relationships:
if relationship1.get("identifier") == identifier:
relationship1.put("isCurated",True)
relationship1.put("curatedPid",pid)
found = True
if not found:
newRelationship = JsonObject()
newRelationship.put("isCurated",True)
newRelationship.put("curatedPid",pid)
newRelationship.put("relationship",relationship.get("relationship"))
newRelationship.put("identifier",identifier)
relationships.add(newRelationship)
istream = ByteArrayInputStream(String(metadataJson.toString(True)).getBytes())
StorageUtils.createOrUpdatePayload(digitalObject,"metadata.json",istream)
def checkRequests(self, checklist_filter=['1'], role_filter='reviewer', exclusive=True, startPage=1):
""" A customised query for arms at arms-review
Get a list of requests filtered by provisioning_checklist
For assessor, it is user based and queries against committee-responses.metadata
"""
workflowStep = "arms-review"
if self.packageType:
req = SearchRequest(self.packageType)
else:
req = SearchRequest("packageType:arms")
req.addParam("fq", 'workflow_step:' + workflowStep)
for item in ['1','2','3','4']:
if item in checklist_filter:
req.addParam("fq", '-provisioning_checklist.' + item + ':null' + ' AND provisioning_checklist.' + item + ':[* TO *]')
else:
if exclusive:
# ensure that brand new submissions (not yet saved by reviewer) are also returned
req.addParam("fq", 'provisioning_checklist.' + item + ':null' + ' OR (*:* -provisioning_checklist.' + item + ':[* TO *])')
req.setParam("sort", "date_object_modified desc, f_dc_title asc")
req.setParam("fl",self.returnFields)
out = ByteArrayOutputStream()
self.indexer.search(req, out)
solrResults = SolrResult(ByteArrayInputStream(out.toByteArray()))
if solrResults:
results = solrResults.getResults()
if results:
packageResults = results
results = self.mergeEvents(packageResults, ["arms_draft","arms_redraft","arms_review","arms_approved","arms_rejected"])
returnArray = JSONArray()
if role_filter.startswith('assessor'):
if role_filter == 'assessor':
query_status = ['new', 'draft']
elif role_filter == 'assessor-assessed':
query_status = ['submitted']
x = Assessment()
x.activate(self.velocityContext)
i = 0
rows = self.recordsPerPage
start = (startPage - 1) * self.recordsPerPage
for r in results:
status = x.queryStatus(r.get("id"))
if status in query_status:
if i >= start and i - start < rows:
if status == 'submitted':
assessment_submitted_date = x.queryMyAttr('date')
if assessment_submitted_date:
r.getJsonObject().put('date', assessment_submitted_date)
returnArray.add(r)
i = i + 1
else:
returnArray = results
self._setPaging(returnArray.size())
return returnArray
else:
return ArrayList()
def _addRelatedOid(self, tfPackageJson, relatedOid):
relatedOids = tfPackageJson.getArray("related.datasets")
if relatedOids is None:
relatedOids = JSONArray()
relatedOidJsonObject = JsonObject()
relatedOidJsonObject.put("oid",relatedOid)
relatedOids.add(relatedOidJsonObject)
jsonObject = tfPackageJson.getJsonObject()
jsonObject.put("related.datasets", relatedOids)
return jsonObject
def _addRelatedOid(self, tfPackageJson, relatedOid):
relatedOids = tfPackageJson.getArray("related.datasets")
if relatedOids is None:
relatedOids = JSONArray()
relatedOidJsonObject = JsonObject()
relatedOidJsonObject.put("oid", relatedOid)
relatedOids.add(relatedOidJsonObject)
jsonObject = tfPackageJson.getJsonObject()
jsonObject.put("related.datasets", relatedOids)
return jsonObject
def getVersions(self, storedObj):
indF = File(storedObj.getPath() + "/Version_Index.json")
versions = []
if indF.exists():
versions = JsonSimple(indF).getJsonArray()
# reverse to the order to from latest to oldest
r = JSONArray()
for s in reversed(versions):
r.add(s)
versions = r
return versions
def listUserAttributes(self):
""" Query HibernateUserAttribute to get the stored user attributes supported by current authentication manager
Return a JSONArray: can be empty if only internal manager is used
"""
authUserAttrbDao = ApplicationContextProvider.getApplicationContext().getBean("hibernateAuthUserAttributeDao")
attributeList = authUserAttrbDao.query("getUserAttributeList",HashMap())
aList = JSONArray()
if attributeList.size() > 0:
filtered = [attribName for attribName in attributeList if attribName not in self.ATTRIB_FILTER]
for a in filtered:
aList.add(a)
return aList
def getVersions(self, storedObj):
indF = File(storedObj.getPath() + "/Version_Index.json")
versions = []
if indF.exists():
versions = JsonSimple(indF).getJsonArray()
# reverse to the order to from latest to oldest
r = JSONArray()
for s in reversed(versions):
r.add(s)
versions = r
return versions
def getVersions(self, storedObj, extension):
versions = []
try:
indF = storedObj.getPayload(extension + "_Version_Index.json")
versions = JsonSimple(indF.open()).getJsonArray()
# reverse to the order to from latest to oldest
r = JSONArray()
for s in reversed(versions):
r.add(s)
versions = r
except:
self.log.debug("Versioning file not found for "+extension +". Perhaps versioning not enabled.")
return versions
def getVersions(self, storedObj, extension):
versions = []
try:
indF = storedObj.getPayload(extension + "_Version_Index.json")
versions = JsonSimple(indF.open()).getJsonArray()
# reverse to the order to from latest to oldest
r = JSONArray()
for s in reversed(versions):
r.add(s)
versions = r
except:
self.log.debug("Versioning file not found for " + extension +
". Perhaps versioning not enabled.")
return versions
def __getUsers(self, oid):
indexer = Services.getIndexer()
req = SearchRequest("id:" + oid)
req.setParam("fl", "security_exception,owner")
out = ByteArrayOutputStream()
indexer.search(req, out)
rtJson = ""
try:
qresult = SolrResult(ByteArrayInputStream(
out.toByteArray())).getResults().get(0)
owner = qresult.getString(None, 'owner')
secException = qresult.getArray('security_exception')
if secException is None:
secException = JSONArray()
self.log.debug("Owner of object: " + owner)
self.log.debug("Viewer(s) of object: " + secException.toString())
if secException.contains(owner):
secException.remove(owner)
return '{"owner":"' + owner + '", "viewers": ' + secException.toString(
) + '}'
except Exception, e:
self.log.error("Error during query/package ownership data" +
str(e))
def listUserAttributes(self):
""" Query HibernateUserAttribute to get the stored user attributes supported by current authentication manager
Return a JSONArray: can be empty if only internal manager is used
"""
authUserAttrbDao = ApplicationContextProvider.getApplicationContext(
).getBean("hibernateAuthUserAttributeDao")
attributeList = authUserAttrbDao.query("getUserAttributeList",
HashMap())
aList = JSONArray()
if attributeList.size() > 0:
filtered = [
attribName for attribName in attributeList
if attribName not in self.ATTRIB_FILTER
]
for a in filtered:
aList.add(a)
return aList
def getUsers(self, k, v):
""" Query HibernateUserAttribute with supported key:value pair against supported attributes
when query against username, it returns a JSON object as there could be only one user.
Otherwise returns a JSONArray of JSON which contains user's attributes but can be empty
"""
if k == "username":
return self.__getUserInfo(v)
users = JSONArray()
parameters = HashMap()
parameters.put("key", k)
parameters.put("value", v)
authUserAttrbDao = ApplicationContextProvider.getApplicationContext().getBean("hibernateAuthUserAttributeDao")
userObjectList = authUserAttrbDao.query("getUserAttributeByKeyAndValueDistinct", parameters)
if userObjectList.size() > 0:
for userObj in userObjectList:
users.add(self.__constructUserAttribs(userObj[0], self.ATTRIB_FILTER))
return users
def __activate__(self, context):
pageSize = 10
self.velocityContext = context
client = OrcidPublicClient()
self.response = context["response"]
self.request = context["request"]
self.writer = self.response.getPrintWriter("text/plain; charset=UTF-8")
givenNames = self.request.getParameter("givenNames")
familyName = self.request.getParameter("familyName")
pageNumber = self.request.getParameter("page")
if pageNumber is None:
pageNumber = "1"
query = ""
if givenNames == "" or givenNames is None:
query = OrcidSearchField.FAMILY_NAME.buildPrefixQuery(familyName)
else:
if familyName == "" or familyName is None:
query = OrcidSearchField.GIVEN_NAMES.buildPrefixQuery(givenNames)
else:
query = OrcidSearchField.FAMILY_NAME.buildPrefixQuery(familyName) + " AND " + OrcidSearchField.GIVEN_NAMES.buildPrefixQuery(givenNames)
results = client.search(query, int(pageNumber)-1, pageSize)
responseObject = JsonObject()
responseObject.put("pageNumber",int(pageNumber))
responseObject.put("totalPages",results.getNumFound().divide(BigInteger(String(str(pageSize)))).add(BigInteger("1")))
responseObject.put("totalFound",results.getNumFound())
recordResults = JSONArray()
for searchResult in results.getOrcidSearchResult():
personalDetails = searchResult.getOrcidProfile().getOrcidBio().getPersonalDetails()
orcidUri = self.getOrcid(searchResult.getOrcidProfile().getOrcidIdentifier(), "uri")
orcid = self.getOrcid(searchResult.getOrcidProfile().getOrcidIdentifier(), "path")
resultObject = JsonObject()
resultObject.put("given_names",personalDetails.getGivenNames())
resultObject.put("family_name",personalDetails.getFamilyName())
resultObject.put("orcid_uri",orcidUri)
resultObject.put("orcid",orcid)
recordResults.add(resultObject)
responseObject.put("search_results",recordResults)
self.writer.println(JsonSimple(responseObject).toString(True))
self.writer.close()
def getJson(self, state = "open"):
title = "%s (%s)" % (self.getName(), self.getCount())
json = JsonSimple()
jsonObj = json.getJsonObject()
attributes = JsonObject()
attributes.put("id", self.getId())
attributes.put("fq", self.getFacetQuery())
attributes.put("title", title)
jsonObj.put("data", title)
jsonObj.put("attributes", attributes)
hasSubFacets = not self.getSubFacets().isEmpty()
if hasSubFacets:
jsonObj.put("state", state)
subFacetList = ArrayList()
for subFacet in self.getSubFacets():
subFacetList.add(subFacet.getJson("closed"))
children = JSONArray()
children.addAll(subFacetList)
jsonObj.put("children", children)
return json
def getAttachedFiles(self, oid):
# Build a query
req = SearchRequest("attached_to:%s" % oid)
req.setParam("rows", "1000")
# Run a search
out = ByteArrayOutputStream()
self.Services.getIndexer().search(req, out)
result = SolrResult(ByteArrayInputStream(out.toByteArray()))
# Process results
docs = JSONArray()
for doc in result.getResults():
attachmentType = self.escapeHtml(WordUtils.capitalizeFully(doc.getFirst("attachment_type").replace("-", " ")))
accessRights = self.escapeHtml(WordUtils.capitalizeFully(doc.getFirst("access_rights")))
entry = JsonObject()
entry.put("filename", self.escapeHtml(doc.getFirst("filename")))
entry.put("attachment_type", attachmentType)
entry.put("access_rights", accessRights)
entry.put("id", self.escapeHtml(doc.getFirst("id")))
docs.add(entry)
return docs
def getJson(self, state="open"):
title = "%s (%s)" % (self.getName(), self.getCount())
json = JsonSimple()
jsonObj = json.getJsonObject()
attributes = JsonObject()
attributes.put("id", self.getId())
attributes.put("fq", self.getFacetQuery())
attributes.put("title", title)
jsonObj.put("data", title)
jsonObj.put("attributes", attributes)
hasSubFacets = not self.getSubFacets().isEmpty()
if hasSubFacets:
jsonObj.put("state", state)
subFacetList = ArrayList()
for subFacet in self.getSubFacets():
subFacetList.add(subFacet.getJson("closed"))
children = JSONArray()
children.addAll(subFacetList)
jsonObj.put("children", children)
return json
def getViewers(self, oid):
indexer = self.services.getIndexer()
req = SearchRequest("id:" + oid)
req.setParam("fl", "security_exception,owner")
out = ByteArrayOutputStream()
indexer.search(req, out)
try:
qresult = SolrResult(ByteArrayInputStream(out.toByteArray())).getResults().get(0)
owner = qresult.getString(None, 'owner')
secException = qresult.getArray('security_exception')
if secException is None:
secException = JSONArray()
self.log.debug("Owner of object: " + owner)
self.log.debug("Viewer(s) of object: " + secException.toString())
if secException.contains(owner):
secException.remove(owner)
return secException
except Exception, e:
self.log.error("Error during query/package ownership data" + str(e))
def getAttachedFiles(self, oid):
# Build a query
req = SearchRequest("attached_to:%s" % oid)
req.setParam("rows", "1000")
# Run a search
out = ByteArrayOutputStream()
self.Services.getIndexer().search(req, out)
result = SolrResult(ByteArrayInputStream(out.toByteArray()))
# Process results
docs = JSONArray()
for doc in result.getResults():
attachmentType = self.escapeHtml(
WordUtils.capitalizeFully(
doc.getFirst("attachment_type").replace("-", " ")))
accessRights = self.escapeHtml(
WordUtils.capitalizeFully(doc.getFirst("access_rights")))
entry = JsonObject()
entry.put("filename", self.escapeHtml(doc.getFirst("filename")))
entry.put("attachment_type", attachmentType)
entry.put("access_rights", accessRights)
entry.put("id", self.escapeHtml(doc.getFirst("id")))
docs.add(entry)
return docs
def getUsers(self, k, v):
""" Query HibernateUserAttribute with supported key:value pair against supported attributes
when query against username, it returns a JSON object as there could be only one user.
Otherwise returns a JSONArray of JSON which contains user's attributes but can be empty
"""
if k == "username":
return self.__getUserInfo(v)
users = JSONArray()
parameters = HashMap()
parameters.put("key", k)
parameters.put("value", v)
authUserAttrbDao = ApplicationContextProvider.getApplicationContext(
).getBean("hibernateAuthUserAttributeDao")
userObjectList = authUserAttrbDao.query(
"getUserAttributeByKeyAndValueDistinct", parameters)
if userObjectList.size() > 0:
for userObj in userObjectList:
users.add(
self.__constructUserAttribs(userObj[0],
self.ATTRIB_FILTER))
return users
def getFilteredAssessments(self, packageType, stageName, filterType, startPage=1):
""" A customised query to use filter to get certain assessment with desired status """
## reference /redbox-rdsi-arms/src/main/config/home/lib/jython/util/Assessment.py for methods
filters = {'assessment-draft': ['new','draft'], 'assessment-submitted':['submitted']}
statusFilter = filters[filterType]
req = SearchRequest("packageType:" + packageType)
req.addParam("fq", 'workflow_step:' + stageName)
req.setParam("sort", "date_object_modified desc, f_dc_title asc")
req.setParam("fl",self.returnFields)
out = ByteArrayOutputStream()
self.indexer.search(req, out)
solrResults = SolrResult(ByteArrayInputStream(out.toByteArray()))
if solrResults:
results = solrResults.getResults()
returnArray = JSONArray()
x = Assessment()
x.activate(self.velocityContext)
i = 0
rows = self.recordsPerPage
start = (startPage - 1) * self.recordsPerPage
for r in results:
status = x.queryStatus(r.get("id"))
if status in statusFilter:
if i >= start and i - start < rows:
assessment_submitted_date = x.queryAttr(r.get("id"), 'date')
if assessment_submitted_date:
r.getJsonObject().put('date', assessment_submitted_date)
returnArray.add(r)
i = i + 1
self._setPaging(returnArray.size())
return returnArray
else:
return ArrayList()
def __getPayloadJsonArray(self, oid, payloadName):
"""
Get the content (JsonArray) of a payload
return the JSONArray or an empty (new) one
"""
storedObj = self.Services.getStorage().getObject(oid)
payloadList = storedObj.getPayloadIdList()
if payloadList.contains(payloadName):
# print "Updating existing"
payloadObj = storedObj.getPayload(payloadName)
payloadJson = JsonSimple(payloadObj.open())
objList = payloadJson.getJsonArray()
else:
# print "Creating new one"
objList = JSONArray()
return objList
def __getUsers(self, oid):
storage = self.services.getStorage()
object = storage.getObject(oid)
objectMetadata = object.getMetadata()
owner = objectMetadata.getProperty("owner")
ownerJson = self.__constructUserJson(owner)
users = self.getViewers(oid,owner)
returningViewers = []
for user in users:
parameters = HashMap()
# print "Checking user= %s" % user
parameters.put("username",user)
userObjectList = self.authUserDao.query("getUser",parameters)
if userObjectList is not None or userObjectList.size() > 0:
returningViewers.append(self.__constructUserJson(user))
return '{"owner":' + ownerJson.toJSONString() + ', "viewers": ' + JSONArray.toJSONString(returningViewers) + '}'
def __getUsers(self, oid):
storage = self.services.getStorage()
object = storage.getObject(oid)
objectMetadata = object.getMetadata()
owner = objectMetadata.getProperty("owner")
ownerJson = self.__constructUserJson(owner)
users = self.getViewers(oid, owner)
returningViewers = []
for user in users:
parameters = HashMap()
# print "Checking user= %s" % user
parameters.put("username", user)
userObjectList = self.authUserDao.query("getUser", parameters)
if userObjectList is not None or userObjectList.size() > 0:
returningViewers.append(self.__constructUserJson(user))
return '{"owner":' + ownerJson.toJSONString(
) + ', "viewers": ' + JSONArray.toJSONString(returningViewers) + '}'
def __activate__(self, context):
try:
self.log = context["log"]
self.response = context["response"]
self.request = context["request"]
self.systemConfig = context["systemConfig"]
self.storage = context["Services"].getStorage()
self.indexer = context["Services"].getIndexer()
self.sessionState = context["sessionState"]
self.sessionState.set("username", "admin")
out = self.response.getPrintWriter("text/plain; charset=UTF-8")
relationshipMapper = ApplicationContextProvider.getApplicationContext().getBean("relationshipMapper")
externalCurationMessageBuilder = ApplicationContextProvider.getApplicationContext().getBean("externalCurationMessageBuilder")
oid = self.request.getParameter("oid")
if oid is None :
identifier = self.request.getParameter("identifier")
oid = self.findOidByIdentifier(identifier)
relationshipType = self.request.getParameter("relationship")
curatedPid = self.request.getParameter("curatedPid")
sourceId = self.request.getParameter("sourceIdentifier")
system = self.request.getParameter("system")
digitalObject = StorageUtils.getDigitalObject(self.storage, oid)
metadataJsonPayload = digitalObject.getPayload("metadata.json")
metadataJsonInstream = metadataJsonPayload.open()
metadataJson = JsonSimple(metadataJsonInstream)
metadataJsonPayload.close()
relationships = metadataJson.getArray("relationships")
found = False
if relationships is None:
relationships = JSONArray()
metadataJson.getJsonObject().put("relationships",relationships)
for relationship in relationships:
if relationship.get("identifier") == sourceId:
relationship.put("isCurated",True)
relationship.put("curatedPid",curatedPid)
found = True
if not found:
relationship = JsonObject()
relationship.put("isCurated",True)
relationship.put("curatedPid",curatedPid)
relationship.put("relationship",relationshipType)
relationship.put("identifier",sourceId)
relationship.put("system",system)
relationships.add(relationship)
out.println(metadataJson.toString(True))
istream = ByteArrayInputStream(String(metadataJson.toString(True)).getBytes())
StorageUtils.createOrUpdatePayload(digitalObject,"metadata.json",istream)
out.close()
finally:
self.sessionState.remove("username")
def searchNla(self):
# Start row
start = self.formData.get("start")
if start is None:
start = "1"
# Row limit
rows = self.formData.get("rows")
if rows is None:
rows = "10"
# Query
query = ""
# Test searches
#query = "pa.surname=\"Smith\""
#query = "cql.anywhere=\"monash\""
if query == "":
# Surname
surname = self.formData.get("surname")
if surname is not None:
query = "pa.surname=\"%s\"" % (surname)
# Firstname
firstName = self.formData.get("firstName")
if firstName is not None:
if query != "":
query += " AND "
query += "pa.firstname=\"%s\"" % (firstName)
if query != "":
query += " AND "
query += "pa.type=\"person\""
# Some basic metadata we already know
self.metadata.put("searchString", query)
self.metadata.put("startRecord", start)
self.metadata.put("rowsRequested", rows)
# Search NLA
self.log.debug("Submitting query to NLA: '{}', Start: '{}', Rows: '{}'", [query, start, rows])
sru = SRUClient()
# If using the NLA's test server, comment out the line above and uncomment the line below
# sru = SRUClient("http://www-test.nla.gov.au/apps/srw/search/peopleaustralia")
response = sru.nlaGetResponseBySearch(query, start, rows)
if response is None:
raise Exception("Error searching NLA. Please check system logs for details.")
self.metadata.put("rowsReturned", response.getRows())
self.metadata.put("totalHits", response.getTotalResults())
identities = NLAIdentity.convertNodesToIdentities(response.getResults())
for id in identities:
idEntry = JsonObject()
idEntry.put("nlaId", id.getId())
idEntry.put("displayName", id.getDisplayName())
idEntry.put("firstName", id.getFirstName())
idEntry.put("surname", id.getSurame())
idEntry.put("institution", id.getInstitution())
knownIds = JSONArray()
idEntry.put("knownIdentities", knownIds)
for knownId in id.getKnownIdentities():
thisId = JsonObject()
thisId.put("displayName", knownId.get("displayName"))
thisId.put("institution", knownId.get("institution"))
knownIds.add(thisId)
self.results.add(idEntry)
return True