Working graph test

test_graph_ops.py

from omero.gateway import BlitzGateway
from omero.sys import Parameters, ParametersI
from omero.model import *
from omero.rtypes import *
from omero import ValidationException
import ConfigParser

from omero.model import ExperimenterI, ProjectI, DatasetI, ImageI, \
                        ScreenI, PlateI, \
                        ProjectDatasetLinkI, DatasetImageLinkI, \
                        ScreenPlateLinkI

# OMERO Detail Config
omero_details = '/Users/dpwrussell/Checkout/Gists/omero_basics/omero_details.cfg'

config = ConfigParser.RawConfigParser()
config.read(omero_details)

HOST = config.get('OMERODetails', 'host')
PORT = config.getint('OMERODetails', 'port')
USERNAME = config.get('OMERODetails', 'username')
PASSWORD = config.get('OMERODetails', 'password')

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
connected = conn.connect()

params = ParametersI()

if not connected:
    import sys
    sys.stderr.write("Error: Connection not available, please check your user name and password.\n")
    sys.exit(1)

images = [x._obj for x in conn.getObjects('Image')]

print('Images remaining: ', len(images))
# datasetId = datasetObj.getId().getValue()

stop = False
other_group_id = 3

def mkP(name):
    project = ProjectI()
    project.setName(rstring(name))
    return conn.getUpdateService().saveAndReturnObject(project)

def mkD(name):
    dataset = DatasetI()
    dataset.setName(rstring(name))
    return conn.getUpdateService().saveAndReturnObject(dataset)

def lnk(x, y):
    if isinstance(x, ProjectI):
        if isinstance(y, DatasetI):
            link = ProjectDatasetLinkI()
    elif isinstance(x, DatasetI):
        if isinstance(y, ImageI):
            link = DatasetImageLinkI()
    link.setParent(x)
    link.setChild(y)
    conn.getUpdateService().saveObject(link)

def rm(x):
    if isinstance(x[0], ProjectI):
        t = 'Project'
    elif isinstance(x[0], DatasetI):
        t = 'Dataset'
    elif isinstance(x[0], ImageI):
        t = 'Image'
    handle = conn.deleteObjects(t, [i.getId().getValue() for i in x], True, False)
    conn._waitOnCmd(handle)

def cg(x, cid=None):
    if isinstance(x[0], ProjectI):
        t = 'Project'
    elif isinstance(x[0], DatasetI):
        t = 'Dataset'
    elif isinstance(x[0], ImageI):
        t = 'Image'
    handle = conn.chgrpObjects(t, [i.getId().getValue() for i in x], other_group_id, cid)
    conn._waitOnCmd(handle)

def get(x):
    if isinstance(x, ProjectI):
        t = 'Project'
    elif isinstance(x, DatasetI):
        t = 'Dataset'
    elif isinstance(x, ImageI):
        t = 'Image'
    return conn.getObject(t, x.getId().getValue())

def getpriass(**kwargs):
    for k, v in kwargs.iteritems():
        val = get(v)
        print(k, val)
        if stop:
            assert(val == None)
    print('---------')

# Clean up Containers
def cleanup():
    # Doing this from the gateway is a complete pigs ear so fall back on HQL
    eid = conn.getUser().getId()
    params = omero.sys.ParametersI()
    params.add('eid', rlong(eid))

    qs = conn.getQueryService()

    # Unlink all images
    q = """
        from DatasetImageLink dilink
        where dilink.details.owner.id = :eid
        """
    res = qs.findAllByQuery(q, params, conn.SERVICE_OPTS)
    for r in res:
        conn.deleteObjectDirect(r)

    # Remove all datasets
    q = """
        from Dataset dataset
        where dataset.details.owner.id = :eid
        """

    res = qs.findAllByQuery(q, params, conn.SERVICE_OPTS)
    for r in res:
        conn.deleteObjectDirect(r)

    # Remove all projects
    q = """
        from Project project
        where project.details.owner.id = :eid
        """

    res = qs.findAllByQuery(q, params, conn.SERVICE_OPTS)
    for r in res:
        conn.deleteObjectDirect(r)


group = conn.getGroupFromContext()
print "Current group: ", group.getName(), group.getId()
conn.SERVICE_OPTS.setOmeroGroup(group.getId())
omerogroup = conn.SERVICE_OPTS.getOmeroGroup()
print "OMERO group: ", omerogroup
print('\n\n')

# If not using cleanup at the start and stopping on errors, images will be
# reused between runs which have already been put into a container hierarchy
# This can lead to an unexpected failure.
# Beware that cleanup removes all DatsetImageLinks, Datasets and Projects
# that belong to the current user in the current group.
# cleanup()

# P1->D1
# Delete P1
# P1 is deleted, D1 becomes an orphan. FAIL
p1 = mkP('P1')
d1 = mkD('D1')
lnk(p1, d1)
rm([p1])
getpriass(p1=p1, d1=d1)

# P1->D1
# P2->D1
# Delete P1
# D1 is not deleted and link P2->D1 remains. FAIL
p1 = mkP('P1')
p2 = mkP('P2')
d1 = mkD('D1')
lnk(p1, d1)
lnk(p2, d1)
rm([p1])
getpriass(p1=p1, d1=d1)

# P1->D1->I1
# P2->D1->I1
# Delete P1
# D1 is not deleted, link P2->D1 remains, but I1 is deleted. FAIL
p1 = mkP('P1')
p2 = mkP('P2')
d1 = mkD('D1')
i1 = images.pop()
lnk(p1, d1)
lnk(p2, d1)
lnk(d1, i1)
rm([p1])
getpriass(p1=p1, d1=d1, i1=i1)

# P1->D1->I1
# P2->D1->I1
# Delete D1
# I1 is deleted. OK
p1 = mkP('P1')
p2 = mkP('P2')
d1 = mkD('D1')
i1 = images.pop()
lnk(p1, d1)
lnk(p2, d1)
lnk(d1, i1)
rm([d1])
getpriass(d1=d1, i1=i1)

# D1->I1
# D2->I1
# Delete D1
# Exception is thrown: FAIL - For some reason not throwing exception here
# but does from webclient and it looks exactly the same!?!
d1 = mkD('D1')
d2 = mkD('D2')
i1 = images.pop()
lnk(d1, i1)
lnk(d2, i1)
try:
    rm([d1])
except Exception as e:
    print(e)
    if stop:
        raise(e)
getpriass(d1=d1, i1=i1)

# D1->I1
# ChGrp D1
# D1 Hierarchy moved entirely: OK
d1 = mkD('D1')
i1 = images.pop()
lnk(d1, i1)
cg([d1])

getpriass(d1=d1, i1=i1)

# P1->D1->I1
# ChGrp P1
# P1 : FAIL: Except that it does not fail in the webclient!!??
p1 = mkP('P1')
d1 = mkD('D1')
i1 = images.pop()
lnk(p1, d1)
lnk(d1, i1)
cg([p1])

getpriass(p1=p1, d1=d1, i1=i1)

# D1->I1
# D2->I1
# ChGrp D1
# Exception (1): FAIL. Good to see that something fails the same
d1 = mkD('D1')
d2 = mkD('D2')
i1 = images.pop()
lnk(d1, i1)
lnk(d2, i1)
try:
    cg([d1])
except omero.CmdError, e:
    print('Exception thrown')
    if stop:
        print(e.err)
        exit(1)

getpriass(d1=d1, i1=i1)

# P1->D1->I1
# D2->I1
# ChGrp P1
# P1 moved, Image moved but orphaned, D1 not moved and orphaned: FAIL. Again
# differet from webclient, this time, image is not moved either.
p1 = mkP('P1')
d1 = mkD('D1')
d2 = mkD('D2')
i1 = images.pop()
lnk(p1, d1)
lnk(d1, i1)
lnk(d2, i1)
cg([p1])

getpriass(p1=p1, d1=d1, i1=i1)

# P1->D1->I1
# P2->D1->I1
# ChGrp D1
# D1 Hierarchy moved entirely: OK
p1 = mkP('P1')
p2 = mkP('P2')
d1 = mkD('D1')
i1 = images.pop()
lnk(p1, d1)
lnk(p2, d1)
lnk(d1, i1)
cg([d1])

getpriass(d1=d1, i1=i1)

# P1->D1->I1
# P2->D1->I1
# ChGrp P1
# P1 moved, Image moved but orphaned, D1 not moved, but not orphaned as in P2: FAIL
# Different from webclient, image not moved either here.
p1 = mkP('P1')
p2 = mkP('P2')
d1 = mkD('D1')
i1 = images.pop()
lnk(p1, d1)
lnk(p2, d1)
lnk(d1, i1)
cg([p1])

getpriass(p1=p1, d1=d1, i1=i1)

# P1->D1
# P2->D1
# ChGrp P1
# P1 moved, D1 not moved, but not orphaned as in P2: FAIL
p1 = mkP('P1')
p2 = mkP('P2')
d1 = mkD('D1')
lnk(p1, d1)
lnk(p2, d1)
cg([p1])

getpriass(p1=p1, d1=d1)

# P1->D1->I1
# P1->D2->I1
# ChGrp P1
# P1 Hierarchy moved entirely: OK. Not ok here, fails. p1 is moved but nothing
# else
p1 = mkP('P1')
d1 = mkD('D1')
d2 = mkD('D2')
i1 = images.pop()
lnk(p1, d1)
lnk(p1, d2)
lnk(d1, i1)
lnk(d2, i1)
cg([p1])

getpriass(p1=p1, d1=d1, d2=d2, i1=i1)