def mask2set(mask):
local = []
remote = []
if PN_LOCAL_UNINIT & mask:
local.append(EndpointState.UNINITIALIZED)
if PN_LOCAL_ACTIVE & mask:
local.append(EndpointState.ACTIVE)
if PN_LOCAL_CLOSED & mask:
local.append(EndpointState.CLOSED)
if PN_REMOTE_UNINIT & mask:
remote.append(EndpointState.UNINITIALIZED)
if PN_REMOTE_ACTIVE & mask:
remote.append(EndpointState.ACTIVE)
if PN_REMOTE_CLOSED & mask:
remote.append(EndpointState.CLOSED)
if local:
local = EnumSet.of(*local)
else:
local = None
if remote:
remote = EnumSet.of(*remote)
else:
remote = None
return local, remote
def mask2set(mask):
local = []
remote = []
if PN_LOCAL_UNINIT & mask:
local.append(EndpointState.UNINITIALIZED)
if PN_LOCAL_ACTIVE & mask:
local.append(EndpointState.ACTIVE)
if PN_LOCAL_CLOSED & mask:
local.append(EndpointState.CLOSED)
if PN_REMOTE_UNINIT & mask:
remote.append(EndpointState.UNINITIALIZED)
if PN_REMOTE_ACTIVE & mask:
remote.append(EndpointState.ACTIVE)
if PN_REMOTE_CLOSED & mask:
remote.append(EndpointState.CLOSED)
if local:
local = EnumSet.of(*local)
else:
local = None
if remote:
remote = EnumSet.of(*remote)
else:
remote = None
return local, remote
def _enums(self, mask):
local = []
if (self.LOCAL_UNINIT | mask):
local.append(EndpointState.UNINITIALIZED)
if (self.LOCAL_ACTIVE | mask):
local.append(EndpointState.ACTIVE)
if (self.LOCAL_CLOSED | mask):
local.append(EndpointState.CLOSED)
remote = []
if (self.REMOTE_UNINIT | mask):
remote.append(EndpointState.UNINITIALIZED)
if (self.REMOTE_ACTIVE | mask):
remote.append(EndpointState.ACTIVE)
if (self.REMOTE_CLOSED | mask):
remote.append(EndpointState.CLOSED)
return EnumSet.of(*local), EnumSet.of(*remote)
def _enums(self, mask):
local = []
if (self.LOCAL_UNINIT | mask):
local.append(EndpointState.UNINITIALIZED)
if (self.LOCAL_ACTIVE | mask):
local.append(EndpointState.ACTIVE)
if (self.LOCAL_CLOSED | mask):
local.append(EndpointState.CLOSED)
remote = []
if (self.REMOTE_UNINIT | mask):
remote.append(EndpointState.UNINITIALIZED)
if (self.REMOTE_ACTIVE | mask):
remote.append(EndpointState.ACTIVE)
if (self.REMOTE_CLOSED | mask):
remote.append(EndpointState.CLOSED)
return EnumSet.of(*local), EnumSet.of(*remote)
def process(tr, parameters, tableBuilder):
#ids = sorted(parameters.get("ids"))
types = parameters.get(
"types") #sample types (tiers) that are requested for the tsv
project = parameters.get("project")
tableBuilder.addHeader(CODE)
tableBuilder.addHeader(SECONDARY_NAME)
tableBuilder.addHeader(SOURCE)
tableBuilder.addHeader(EXTERNAL_ID)
tableBuilder.addHeader(SAMPLE_TYPE)
tableBuilder.addHeader(XML)
tableBuilder.addHeader(TIER)
#search all samples of project
search = tr.getSearchService()
sc = SearchCriteria()
pc = SearchCriteria()
pc.addMatchClause(
SearchCriteria.MatchClause.createAttributeMatch(
SearchCriteria.MatchClauseAttribute.PROJECT, project))
sc.addSubCriteria(SearchSubCriteria.createExperimentCriteria(pc))
fetchOptions = EnumSet.of(SampleFetchOption.ANCESTORS,
SampleFetchOption.PROPERTIES)
allSamples = search.searchForSamples(sc, fetchOptions)
#filter all samples by types
samples = []
for s in allSamples:
if s.getSampleType() in types:
samples.append(s)
#sort remaining samples-
samples = sorted(samples)
voc = search.getVocabulary("Q_NCBI_TAXONOMY")
for s in samples:
code = sample.getCode()
row = tableBuilder.addRow()
row.setCell(CODE, code)
row.setCell(SECONDARY_NAME,
sample.getPropertyValue("Q_SECONDARY_NAME"))
row.setCell(SOURCE, fetchSource([sample], voc.getTerms(), []))
row.setCell(EXTERNAL_ID, sample.getPropertyValue("Q_EXTERNALDB_ID"))
extrType = sample.getPropertyValue("Q_PRIMARY_TISSUE")
if not extrType:
extrType = sample.getPropertyValue("Q_SAMPLE_TYPE")
if not extrType:
extrType = ""
if extrType == "CELL_LINE":
extrType = sample.getPropertyValue("Q_TISSUE_DETAILED")
row.setCell(SAMPLE_TYPE, extrType)
row.setCell(XML, sample.getPropertyValue("Q_PROPERTIES"))
row.setCell(TIER, sample.getSampleType())
def endpoint_state(impl):
return set2mask(EnumSet.of(impl.getLocalState()),
EnumSet.of(impl.getRemoteState()))
def endpoint_state(impl):
return set2mask(EnumSet.of(impl.getLocalState()),
EnumSet.of(impl.getRemoteState()))