def marshal_projects(conn,
mapann_value,
query=False,
mapann_ns=[],
mapann_names=[],
group_id=-1,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
''' Marshals projects
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
projects = []
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
query=query,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
q = """
select new map(mv.value as value,
project.id as id,
project.name as name,
project.details.owner.id as ownerId,
project as project_details_permissions,
count(distinct dataset.id) as childCount,
count(distinct i.id) as imgCount)
from ImageAnnotationLink ial join ial.child a join a.mapValue mv
join ial.parent i join i.datasetLinks dil
join dil.parent dataset join dataset.projectLinks pl
join pl.parent project
where %s
group by project.id, project.name, mv.value
order by lower(project.name), project.id
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
c = e[0]['imgCount']
e = [
e[0]['id'],
"%s (%d)" % (e[0]["name"], c), e[0]['ownerId'],
e[0]['project_details_permissions'], e[0]['childCount']
]
ms = _marshal_screen(conn, e[0:5])
extra = {'extra': {'counter': c}}
if mapann_value is not None:
extra['extra']['value'] = v
ms.update(extra)
projects.append(ms)
return projects
def marshal_screens(conn,
mapann_value,
query=False,
mapann_ns=[],
mapann_names=[],
group_id=-1,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
''' Marshals screens
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
screens = []
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
query=query,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
# TODO: Joining wellsample should be enough since wells are annotated
# with the same annotations as images. In the future if that changes,
# query has to be restored to:
# - count(distinct i.id) as imgCount)
# - from ImageAnnotationLink ial join ial.child a join a.mapValue mv
# - join ial.parent i join i.wellSamples ws join ws.well w
# - join w.plate pl join pl.screenLinks sl join sl.parent screen
qs = conn.getQueryService()
q = """
select new map(mv.value as value,
screen.id as id,
screen.name as name,
screen.details.owner.id as ownerId,
screen as screen_details_permissions,
count(distinct pl.id) as childCount,
count(distinct ws.id) as imgCount)
from WellAnnotationLink wal join wal.child a join a.mapValue mv
join wal.parent w join w.wellSamples ws
join w.plate pl join pl.screenLinks sl
join sl.parent screen
where %s
group by screen.id, screen.name, mv.value
order by lower(screen.name), screen.id
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
c = e[0]['imgCount']
e = [
e[0]['id'],
"%s (%d)" % (e[0]['name'], c), e[0]['ownerId'],
e[0]['screen_details_permissions'], e[0]['childCount']
]
ms = _marshal_screen(conn, e[0:5])
extra = {'extra': {'counter': c}}
if mapann_value is not None:
extra['extra']['value'] = v
ms.update(extra)
screens.append(ms)
return screens
def marshal_screens(conn, mapann_value, query=False,
mapann_ns=[], mapann_names=[],
group_id=-1, experimenter_id=-1,
page=1, limit=settings.PAGE):
''' Marshals screens
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
screens = []
params, where_clause = _set_parameters(
mapann_ns=mapann_ns, mapann_names=mapann_names,
query=query, mapann_value=mapann_value,
params=None, experimenter_id=experimenter_id,
page=page, limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
# TODO: Joining wellsample should be enough since wells are annotated
# with the same annotations as images. In the future if that changes,
# query has to be restored to:
# - count(distinct i.id) as imgCount)
# - from ImageAnnotationLink ial join ial.child a join a.mapValue mv
# - join ial.parent i join i.wellSamples ws join ws.well w
# - join w.plate pl join pl.screenLinks sl join sl.parent screen
qs = conn.getQueryService()
q = """
select new map(mv.value as value,
screen.id as id,
screen.name as name,
screen.details.owner.id as ownerId,
screen as screen_details_permissions,
count(distinct pl.id) as childCount,
count(distinct ws.id) as imgCount)
from WellAnnotationLink wal join wal.child a join a.mapValue mv
join wal.parent w join w.wellSamples ws
join w.plate pl join pl.screenLinks sl
join sl.parent screen
where %s
group by screen.id, screen.name, mv.value
order by lower(screen.name), screen.id
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
c = e[0]['imgCount']
e = [e[0]['id'],
"%s (%d)" % (e[0]['name'], c),
e[0]['ownerId'],
e[0]['screen_details_permissions'],
e[0]['childCount']]
ms = _marshal_screen(conn, e[0:5])
extra = {'extra': {'counter': c}}
if mapann_value is not None:
extra['extra']['value'] = v
ms.update(extra)
screens.append(ms)
return screens
def marshal_projects(conn, mapann_value, query=False,
mapann_ns=[], mapann_names=[],
group_id=-1, experimenter_id=-1,
page=1, limit=settings.PAGE):
''' Marshals projects
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
projects = []
params, where_clause = _set_parameters(
mapann_ns=mapann_ns, mapann_names=mapann_names,
query=query, mapann_value=mapann_value,
params=None, experimenter_id=experimenter_id,
page=page, limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
q = """
select new map(mv.value as value,
project.id as id,
project.name as name,
project.details.owner.id as ownerId,
project as project_details_permissions,
count(distinct dataset.id) as childCount,
count(distinct i.id) as imgCount)
from ImageAnnotationLink ial join ial.child a join a.mapValue mv
join ial.parent i join i.datasetLinks dil
join dil.parent dataset join dataset.projectLinks pl
join pl.parent project
where %s
group by project.id, project.name, mv.value
order by lower(project.name), project.id
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
v = e[0]['value']
c = e[0]['imgCount']
e = [e[0]['id'],
"%s (%d)" % (e[0]["name"], c),
e[0]['ownerId'],
e[0]['project_details_permissions'],
e[0]['childCount']]
ms = _marshal_screen(conn, e[0:5])
extra = {'extra': {'counter': c}}
if mapann_value is not None:
extra['extra']['value'] = v
ms.update(extra)
projects.append(ms)
return projects
def marshal_screens(conn,
mapann_ns=[],
mapann_names=[],
mapann_value=None,
mapann_query=None,
group_id=-1,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
''' Marshals screens
@param conn OMERO gateway.
@type conn L{omero.gateway.BlitzGateway}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param group_id The Group ID to filter by or -1 for all groups,
defaults to -1
@type group_id L{long}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to 1
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
screens = []
params, where_clause = _set_parameters(mapann_ns=mapann_ns,
mapann_names=mapann_names,
mapann_query=mapann_query,
mapann_value=mapann_value,
params=None,
experimenter_id=experimenter_id,
page=page,
limit=limit)
service_opts = deepcopy(conn.SERVICE_OPTS)
# Set the desired group context
if group_id is None:
group_id = -1
service_opts.setOmeroGroup(group_id)
qs = conn.getQueryService()
q = """
select new map(screen.id as id,
screen.name as name,
screen.details.owner.id as ownerId,
screen as screen_details_permissions,
count(distinct p.id) as childCount,
count(distinct i.id) as imgCount)
from ImageAnnotationLink ial join ial.child a join a.mapValue mv
join ial.parent i join i.wellSamples ws join ws.well w
join w.plate p join p.screenLinks sl join sl.parent screen
where %s
group by screen.id, screen.name
order by lower(screen.name), screen.id
""" % (" and ".join(where_clause))
logger.debug("HQL QUERY: %s\nPARAMS: %r" % (q, params))
for e in qs.projection(q, params, service_opts):
e = unwrap(e)
e = [
e[0]["id"],
"%s (%d)" % (e[0]["name"], e[0]["imgCount"]), e[0]["ownerId"],
e[0]["screen_details_permissions"], e[0]["childCount"]
]
ms = _marshal_screen(conn, e[0:5])
ms.update({'extra': {'value': mapann_value}})
screens.append(ms)
return screens