def test_annotateAndAnnotated(self):
# There's a bug somewhere which means annotating the table with the
# version annotation, then using the table as a FileAnnotation on
# an object, causes the version annotation to be lost
# Closing and reopening the table seems to work (see
# FeatureTable.createTable)
cli, sess = self.create_client()
ft = FeatureTable(client=cli, tableName=self.tableName)
fts = ['a [0]', 'a [1]', 'b [0]']
ft.createTable(fts, version=self.version)
tid = ft.tc.tableId
self.assertEqual(self.version, unwrapVersion(ft.versiontag))
vertag = WndcharmStorage.getVersion(ft.conn, 'OriginalFile', tid)
self.assertEqual(self.version, unwrapVersion(vertag))
p = omero.model.ProjectI()
p.setName(wrap('tmp'))
p = self.sess.getUpdateService().saveAndReturnObject(p)
pid = unwrap(p.getId())
p = ft.conn.getObject('Project', pid)
WndcharmStorage.addFileAnnotationTo(ft.tc, p)
vertag = WndcharmStorage.getVersion(ft.conn, 'OriginalFile', tid)
self.assertEqual(self.version, unwrapVersion(vertag))
self.delete('/Project', pid)
self.delete('/OriginalFile', tid)
def test_getClassifierTagSet(self):
pid = self.create_project('addTagTo')
p = self.conn.getObject('Project', pid)
classifierName = 'getClassifierTagSet'
instanceName = str(uuid.uuid1())
labels = ['A', 'B']
WndcharmStorage.createClassifierTagSet(
self.conn, classifierName, instanceName, labels, p)
tagset = WndcharmStorage.getClassifierTagSet(
classifierName, instanceName, p)
self.assertIsNotNone(tagset)
self.assertEqual(tagset.getNs(),
omero.constants.metadata.NSINSIGHTTAGSET)
tags = list(self.conn.getObjects('TagAnnotation', attributes={
'ns': classifierName + '/' + instanceName}))
self.assertEqual(len(tags), 2)
self.assertEqual(sorted([t.getValue() for t in tags]), labels)
for t in tags:
self.assertEqual(t.getParent(), tagset)
# Delete the project and tagset but not the child tags
self.delete('/Project', pid)
self.delete('/Annotation', [t.id for t in tags])
def test_deleteTags(self):
us = self.conn.getUpdateService()
tagSet = omero.model.TagAnnotationI()
classifierName = 'getClassifierTagSet'
instanceName = str(uuid.uuid1())
instanceNs = classifierName + '/' + instanceName
tagSet.setTextValue(wrap(instanceNs));
tagSet.setNs(wrap(omero.constants.metadata.NSINSIGHTTAGSET));
tagSet = us.saveAndReturnObject(tagSet);
tag = omero.model.TagAnnotationI()
tag.setTextValue(wrap(str(uuid.uuid1())));
tag.setNs(wrap(instanceNs));
tag = us.saveAndReturnObject(tag);
link = omero.model.AnnotationAnnotationLinkI()
link.setChild(tag)
link.setParent(tagSet)
link = us.saveAndReturnObject(link)
self.assertIsNotNone(self.getObject('TagAnnotation', tagSet.id))
self.assertIsNotNone(self.getObject('TagAnnotation', tag.id))
self.assertIsNotNone(self.getObject(
'AnnotationAnnotationLink', link.id))
WndcharmStorage.deleteTags(self.conn, tagSet)
self.assertIsNone(self.getObject('TagAnnotation', tagSet.id))
self.assertIsNone(self.getObject('TagAnnotation', tag.id))
self.assertIsNone(self.getObject(
'AnnotationAnnotationLink', link.id))
def test_unlinkAnnotations(self):
us = self.conn.getUpdateService()
f = omero.model.OriginalFileI()
f.setName(wrap(str(uuid.uuid1())))
f.setPath(wrap(str(uuid.uuid1())))
f = self.sess.getUpdateService().saveAndReturnObject(f)
tag = omero.model.TagAnnotationI()
tag.setTextValue(wrap(str(uuid.uuid1())));
tag = us.saveAndReturnObject(tag);
link = omero.model.OriginalFileAnnotationLinkI()
link.setChild(tag)
link.setParent(f)
link = us.saveAndReturnObject(link)
self.assertIsNotNone(self.getObject('TagAnnotation', tag.id))
self.assertIsNotNone(self.getObject('OriginalFile', f.id))
self.assertIsNotNone(self.getObject(
'OriginalFileAnnotationLink', link.id))
file = self.conn.getObject('OriginalFile', unwrap(f.id))
WndcharmStorage.unlinkAnnotations(self.conn, file)
self.assertIsNotNone(self.getObject('TagAnnotation', tag.id))
self.assertIsNotNone(self.getObject('OriginalFile', file.id))
self.assertIsNone(self.getObject('OriginalFileAnnotationLink', link.id))
self.delete('/OriginalFile', unwrap(f.id))
self.delete('/Annotation', unwrap(tag.id))
def test_addCommentTo(self):
pid = self.create_project('addCommentTo')
txt = 'This is a comment'
WndcharmStorage.addCommentTo(self.conn, txt, 'Project', pid)
proj = self.conn.getObject('Project', pid)
a = proj.getAnnotation()
self.assertIsInstance(a._obj, omero.model.CommentAnnotation)
self.assertEqual(unwrap(a.getTextValue()), txt)
self.delete('/Project', pid)
def test_getAttachedTableFile(self):
pid = self.create_project('addFileAnnotationTo')
p = self.conn.getObject('Project', pid)
tc = self.Tc(self.conn)
fid = unwrap(tc.table.getOriginalFile().getId())
self.assertIsNone(WndcharmStorage.getAttachedTableFile(tc, p))
WndcharmStorage.addFileAnnotationTo(tc, p)
self.assertIsNotNone(WndcharmStorage.getAttachedTableFile(tc, p))
tc.close()
self.delete('/Project', pid)
def test_addFileAnnotationTo(self):
pid = self.create_project('addFileAnnotationTo')
p = self.conn.getObject('Project', pid)
tc = self.Tc(self.conn)
fid = unwrap(tc.table.getOriginalFile().getId())
WndcharmStorage.addFileAnnotationTo(tc, p)
proj = self.conn.getObject('Project', pid)
a = proj.getAnnotation()
self.assertIsInstance(a._obj, omero.model.FileAnnotation)
self.assertEqual(unwrap(a.getFile().getId()), fid)
tc.close()
self.delete('/Project', pid)
def test_addTagTo(self):
pid = self.create_project('addTagTo')
txt = 'This is a tag'
tid = self.create_tag(txt)
tag = omero.model.TagAnnotationI(tid, False)
WndcharmStorage.addTagTo(self.conn, tag, 'Project', pid)
proj = self.conn.getObject('Project', pid)
a = proj.getAnnotation()
self.assertIsInstance(a._obj, omero.model.TagAnnotation)
self.assertEqual(unwrap(a.getTextValue()), txt)
self.assertEqual(unwrap(a.getId()), tid)
self.delete('/Project', pid)
def checkClassifierTablesVersion(self, ct):
self.assertEqual(unwrapVersion(ct.versiontag), self.version)
verF = WndcharmStorage.getVersion(
ct.tcF.conn, 'OriginalFile', ct.tcF.tableId)
self.assertEqual(unwrapVersion(verF), self.version)
verW = WndcharmStorage.getVersion(
ct.tcW.conn, 'OriginalFile', ct.tcW.tableId)
self.assertEqual(unwrapVersion(verW), self.version)
verL = WndcharmStorage.getVersion(
ct.tcL.conn, 'OriginalFile', ct.tcL.tableId)
self.assertEqual(unwrapVersion(verL), self.version)
def test_featureSizes(self):
ftsz = WndcharmStorage.featureSizes(['a b [12]', 'c d [3]', 'a b [14]'])
self.assertEqual(len(ftsz.keys()), 2)
self.assertIn('a b', ftsz)
self.assertIn('c d', ftsz)
self.assertEqual(ftsz['a b'], 15)
self.assertEqual(ftsz['c d'], 4)
def test_addTextFileAnnotationTo(self):
pid = self.create_project('addTextFileAnnotationTo')
txt = 'This is\nsome text.'
filename = 'addTextFileAnnotationTo.txt'
description = 'Description of addTextFileAnnotationTo.txt'
WndcharmStorage.addTextFileAnnotationTo(
self.conn, txt, 'Project', pid, filename, description)
p = self.conn.getObject('Project', pid)
anns = list(p.listAnnotations())
self.assertEqual(len(anns), 1)
a = anns[0]
self.assertEqual(a.getFileName(), filename)
self.assertEqual(a.getDescription(), description)
self.assertEqual(a.getFileSize(), len(txt))
self.assertEqual(list(a.getFileInChunks())[0], txt)
self.delete('/Annotation', a.getId())
self.delete('/Project', pid)
def test_createTable(self):
tid = self.create_table()
ft = FeatureTable(client=self.cli, tableName=self.tableName)
ft.openTable(tid)
self.assertEqual(self.version, unwrapVersion(ft.versiontag))
vertag = WndcharmStorage.getVersion(ft.conn, 'OriginalFile', tid)
self.assertEqual(self.version, unwrapVersion(vertag))
headers = ft.tc.getHeaders()
self.assertEqual(len(headers), 3)
self.assertEqual([h.name for h in headers], ['id', 'a', 'b'])
self.assertEqual([h.size for h in headers[1:]], [2, 1])
def test_createClassifierTagSet(self):
classifierName = 'createClassifierTagSet'
instanceName = str(uuid.uuid1())
labels = ['A', 'B']
WndcharmStorage.createClassifierTagSet(
self.conn, classifierName, instanceName, labels)
tagset = list(self.conn.getObjects('TagAnnotation', attributes={
'textValue': classifierName + '/' + instanceName,
'ns': omero.constants.metadata.NSINSIGHTTAGSET}))
self.assertEqual(len(tagset), 1)
tagset = tagset[0]
tags = list(self.conn.getObjects('TagAnnotation', attributes={
'ns': classifierName + '/' + instanceName}))
self.assertEqual(len(tags), 2)
self.assertEqual(sorted([t.getValue() for t in tags]), labels)
for t in tags:
self.assertEqual(t.getParent(), tagset)
self.delete('/Annotation', [tagset.getId()] + [t.id for t in tags])
def test_getVersion(self):
version = str(uuid.uuid1())
tableid = self.create_table()
file = omero.model.OriginalFileI(tableid, False)
version = str(uuid.uuid1())
tagid = self.create_tag(version, WndcharmStorage.WNDCHARM_VERSION_NAMESPACE)
tag = omero.model.TagAnnotationI(tagid, False)
link = omero.model.OriginalFileAnnotationLinkI()
link.setChild(tag)
link.setParent(file)
link = self.sess.getUpdateService().saveAndReturnObject(link)
retrieved = WndcharmStorage.getVersion(
self.conn, 'OriginalFile', unwrap(file.getId()))
self.assertEqual(unwrapVersion(retrieved), version)
def test_assertVersionMatch(self):
class MockVersion:
def __init__(self, version):
self.version = version
def getTextValue(self):
return self.version
v1 = MockVersion('12.345')
v2 = MockVersion('12.345')
v3 = MockVersion('543.21')
WndcharmStorage.assertVersionMatch(v1, v2)
WndcharmStorage.assertVersionMatch(v1, v2.getTextValue())
WndcharmStorage.assertVersionMatch(v1.getTextValue(), v2)
self.assertRaises(
WndcharmStorage.WndcharmStorageError, WndcharmStorage.assertVersionMatch,
v1, v3)
def test_versionAnnotation(self):
version = str(uuid.uuid1())
created = WndcharmStorage.createVersionAnnotation(self.conn, version)
retrieved = WndcharmStorage.getVersionAnnotation(self.conn, version)
self.assertEqual(unwrap(created.getNs()),
WndcharmStorage.WNDCHARM_VERSION_NAMESPACE)
self.assertEqual(unwrapVersion(created), version)
self.assertEqual(unwrap(retrieved.getNs()),
WndcharmStorage.WNDCHARM_VERSION_NAMESPACE)
self.assertEqual(unwrapVersion(retrieved), version)
pid = self.create_project('versionAnnotation')
self.assertIsNone(WndcharmStorage.getVersion(self.conn, 'Project', pid))
WndcharmStorage.addTagTo(self.conn, retrieved, 'Project', pid)
a = WndcharmStorage.getVersion(self.conn, 'Project', pid)
self.assertEqual(unwrap(a.getNs()),
WndcharmStorage.WNDCHARM_VERSION_NAMESPACE)
self.assertEqual(unwrapVersion(a), version)
self.delete('/Project', pid)
def test_insert_channel_name(self):
r = WndcharmStorage.insert_channel_name('a (b ()) [3]', 'ch')
self.assertEqual(r, 'a (b (ch)) [3]')
def test_datasetGenerator(self):
WndcharmStorage.datasetGenerator(conn, dataType, ids)
def test_parseFeatureName(self):
r = WndcharmStorage.parseFeatureName('a b [321]')
self.assertEqual(len(r), 2)
self.assertEqual(r[0], 'a b')
self.assertEqual(r[1], 321)
def test_createFeatureName(self):
r = WndcharmStorage.createFeatureName('a b', 321)
self.assertEqual(r, 'a b [321]')
