def testSessionPath(self):
tests = [("archive", "D_1000000000", "session_test/12345")]
for (fs, dataSetId, session_dir) in tests:
logger.debug("File source %s dataSetId %s session dir %s" % (fs, dataSetId, session_dir))
fileSource = ("session", "wf-session", "session-download")
for fs in fileSource:
pI = PathInfo(siteId=self.__siteId, sessionPath=session_dir)
fp = pI.getDirPath(dataSetId=dataSetId, fileSource=fs)
logger.debug("session path %s" % fp)
self.assertIsNotNone(fp, "Failed to get session path")
def testGetStandardPaths(self):
"""Test getting standard file names within session paths."""
ok = True
# fileSource, id, partionId, versionId
tests = [
("archive", "D_1000000000", None, 1, "latest"),
("archive", "D_1000000000", None, "latest", "latest"),
("archive", "D_1000000000", None, "next", "latest"),
("archive", "D_1000000000", None, "previous", "latest"),
("deposit", "D_1000000000", None, 1, "latest"),
]
eId = "1"
for (fs, dataSetId, wfInst, pId, vId) in tests:
logger.debug("File source %s dataSetId %s partno %s wfInst %s version %s" % (fs, dataSetId, pId, wfInst, vId))
pI = PathInfo(siteId=self.__siteId)
pI.setDebugFlag(False)
#
fp = pI.getModelPdbxFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Model path (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find model file - default")
fp = pI.getModelPdbxFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId, mileStone="deposit")
logger.debug("Model path (deposit) (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find model file - deposit")
fp = pI.getModelPdbxFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId, mileStone="upload")
logger.debug("Model path (upload) (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find model file - upload")
fp = pI.getModelPdbFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Model path (PDB): %s" % fp)
self.assertIsNotNone(fp, "Failed to find PDB model file")
fp = pI.getStructureFactorsPdbxFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("SF path (pdbx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find SF file")
fp = pI.getPolyLinkFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Link dist (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find PDBx model file")
fp = pI.getPolyLinkReportFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Link Report dist (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find link report file")
fp = pI.getSequenceStatsFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Sequence stats (PIC): %s" % fp)
self.assertIsNotNone(fp, "Failed to find sequence stats file")
fp = pI.getSequenceAlignFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Sequence align (PIC): %s" % fp)
self.assertIsNotNone(fp, "Failed to find sequence align file")
fp = pI.getReferenceSequenceFilePath(dataSetId, entityId=eId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Reference match entity %s (PDBx): %s" % (eId, fp))
self.assertIsNotNone(fp, "Failed to find reference sequence file")
fp = pI.getSequenceAssignmentFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Sequence assignment (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find sequence assignment")
fp = pI.getAssemblyAssignmentFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Assembly assignment (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find assembly assignment")
fp = pI.getBlastMatchFilePath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId)
logger.debug("Blast match (xml): %s" % fp)
self.assertIsNotNone(fp, "Failed to find blast match file")
fp = pI.getFilePath(dataSetId, wfInstanceId=wfInst, contentType="seqdb-match", formatType="pdbx", fileSource=fs, versionId=vId, partNumber=pId, mileStone=None)
logger.debug("Sequence match (getFilePath) (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find seq-db match")
#
fp = pI.getFilePathContentTypeTemplate(dataSetId, wfInstanceId=wfInst, contentType="model", fileSource=fs)
logger.debug("Model template: %s" % fp)
self.assertIsNotNone(fp, "Failed to find model template")
fp = pI.getArchivePath(dataSetId)
logger.debug("getArchivePath (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find dir path")
fp = pI.getDepositPath(dataSetId)
logger.debug("getDepositPath (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find deposit path")
fp = pI.getInstancePath(dataSetId, wfInstanceId="W_099")
logger.debug("getWfInstancePath (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find wf instance path")
fp = pI.getInstanceTopPath(
dataSetId,
)
logger.debug("getWfInstanceTopPath (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find wf Top instance path")
fp = pI.getTempDepPath(dataSetId)
logger.debug("getTempDepPath): %s" % fp)
self.assertIsNotNone(fp, "Failed to find TempDep path")
#
fp = pI.getDirPath(dataSetId, wfInstanceId=wfInst, fileSource=fs, versionId=vId, partNumber=pId, mileStone=None)
logger.debug("Sequence match (getDirPath) (PDBx): %s" % fp)
self.assertIsNotNone(fp, "Failed to find dir path")
ft = pI.getFilePathVersionTemplate(dataSetId, wfInstanceId=wfInst, contentType="em-volume", formatType="map", fileSource="archive", partNumber=pId, mileStone=None)
logger.debug("EM volume version template: %r" % ft)
ft = pI.getFilePathPartitionTemplate(dataSetId, wfInstanceId=wfInst, contentType="em-mask-volume", formatType="map", fileSource="archive", mileStone=None)
logger.debug("EM mask partition template: %r" % ft)
self.assertIsNotNone(ft, "Failed to mask model file")
self.assertEqual(ok, True)