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Fixed race condition bug in tables #292

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Jul 9, 2021
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9 changes: 6 additions & 3 deletions src/omero/hdfstorageV2.py
Original file line number Diff line number Diff line change
Expand Up @@ -156,12 +156,15 @@ def addOrThrow(self, hdfpath, hdfstorage, read_only=False):
return hdffile

@locked
def getOrCreate(self, hdfpath, read_only=False):
def getOrCreate(self, hdfpath, table, read_only=False):
storage = None
try:
return self.__paths[hdfpath]
storage = self.__paths[hdfpath]
except KeyError:
# Adds itself to the global list
return HdfStorage(hdfpath, self._lock, read_only=read_only)
storage = HdfStorage(hdfpath, self._lock, read_only=read_only)
storage.incr(table)
return storage

@locked
def remove(self, hdfpath, hdffile):
Expand Down
12 changes: 6 additions & 6 deletions src/omero/tables.py
Original file line number Diff line number Diff line change
Expand Up @@ -50,23 +50,21 @@ class TableI(omero.grid.Table, omero.util.SimpleServant):
Spreadsheet implementation based on pytables.
"""

def __init__(self, ctx, file_obj, factory, storage, uuid="unknown",
def __init__(self, ctx, file_obj, file_path, factory, storage_factory, read_only=False, uuid="unknown",
call_context=None, adapter=None):
self.id = Ice.Identity()
self.id.name = uuid
self.uuid = uuid
self.file_obj = file_obj
self.factory = factory
self.storage = storage
self.storage = storage_factory.getOrCreate(file_path, self, read_only)
self.call_context = call_context
self.adapter = adapter
self.can_write = factory.getAdminService().canUpdate(
file_obj, call_context)
omero.util.SimpleServant.__init__(self, ctx)

self.stamp = time.time()
self.storage.incr(self)

self._closed = False

if (not self.file_obj.isLoaded() or
Expand Down Expand Up @@ -531,8 +529,10 @@ def getTable(self, file_obj, factory, current=None):
if not p.exists():
p.makedirs()

storage = self._storage_factory.getOrCreate(file_path, self.read_only)
table = TableI(self.ctx, file_obj, factory, storage,
table = TableI(self.ctx, file_obj,file_path,
factory,
self._storage_factory,
read_only=self.read_only,
uuid=Ice.generateUUID(),
call_context=current.ctx,
adapter=current.adapter)
Expand Down
27 changes: 15 additions & 12 deletions test/unit/tablestest/test_servants.py
Original file line number Diff line number Diff line change
Expand Up @@ -192,6 +192,15 @@ def decr(self, *args):
def size(self):
return 0

class mock_storage_factory():
def __init__(self):
self.storages = []

def add_storage(self, storage):
self.storages.append(storage)

def getOrCreate(self, hdfpath, table, read_only=False):
return self.storages.pop()

class TestTables(TestCase):

Expand Down Expand Up @@ -307,27 +316,21 @@ def testTableOriginalFileLoaded(self):
f2.details.group = omero.model.ExperimenterGroupI(1, False)
self.sf.return_values.append(f2)
storage = mock_storage()
storage_factory = mock_storage_factory()
storage_factory.add_storage(storage)
self.ctx.newSession()
table = omero.tables.TableI(self.ctx, f1, self.sf, storage)
table = omero.tables.TableI(self.ctx, f1, 'dummy/path', self.sf, storage_factory)
assert table.file_obj.details.group

def testTableIncrDecr(self):
f = omero.model.OriginalFileI(1, True)
f.details.group = omero.model.ExperimenterGroupI(1, False)
storage = mock_storage()
table = omero.tables.TableI(self.ctx, f, self.sf, storage)
assert storage.up
table.cleanup()
assert storage.down

def testTablePreInitialized(self):
f = omero.model.OriginalFileI(1, True)
f.details.group = omero.model.ExperimenterGroupI(1, False)
mocktable = self.testTables()
table1 = mocktable.table
storage = table1.storage
storage.initialize([LongColumnI("a", None, [])])
table2 = omero.tables.TableI(self.ctx, f, self.sf, storage)
storage_factory = self._TestTables__tables[0]._storage_factory
table2 = omero.tables.TableI(self.ctx, f, str(storage._HdfStorage__hdf_path), self.sf, storage_factory)
table2.cleanup()
table1.cleanup()

Expand Down Expand Up @@ -372,12 +375,12 @@ def testErrorInStorage(self):
self.repofile(self.sf.db_uuid)
of = omero.model.OriginalFileI(1, False)
self.sf.return_values.append(of)
self.sf.return_values.append(of)

internal_repo = mock_internal_repo(self.tmp)
f = open(internal_repo.path, "w")
f.write("this file is not HDF")
f.close()

tables = self.tablesI(internal_repo)
pytest.raises(omero.ValidationException, tables.getTable, of, self.sf,
self.current)
Expand Down