Beispiel #1
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 def get_vessel(self, label):
   """
   Return the Vessel object labeled 'label' or None if nothing
   matches 'label'. A label 'foo:A1' is interpreted as well 'A1' of
   plate 'foo'.
   """
   import re
   if re.match(r'^.*::+.*$', label):
     # Labels like SAMPLE::PROTOCOL must be considered as a single label
     parts = [label]
   else:
     parts = label.split(':')
   if len(parts) == 1:
     query = 'select t from Tube t where t.label = :label'
     pars = self.kb.ome_query_params({'label': wp.ome_wrap(label, wp.STRING)})
     result = self.kb.ome_operation("getQueryService", "findByQuery",
                                    query, pars)
     return None if result is None else self.kb.factory.wrap(result)
   elif len(parts) == 2:
     query = """select pw from PlateWell pw join fetch pw.container as ct
     where pw.label = :wlabel and ct.label = :clabel
     """
     pars = self.kb.ome_query_params({
       'clabel': wp.ome_wrap(parts[0], wp.STRING),
       'wlabel': wp.ome_wrap(parts[1], wp.STRING),
       })
     result = self.kb.ome_operation("getQueryService", "findByQuery",
                                    query, pars)
     return None if result is None else self.kb.factory.wrap(result)
   else:
     raise ValueError('Bad label %s value' % label)
Beispiel #2
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 def find_all_by_query(self, query, params, factory):
   if params:
     xpars = {}
     for k,v in params.iteritems():
       xpars[k] = ome_wrap(*v) if type(v) == tuple else ome_wrap(v)
     pars = self.ome_query_params(xpars)
   else:
     pars = None
   result = self.ome_operation("getQueryService", "findAllByQuery",
                               query, pars)
   return [] if result is None else [factory.wrap(r) for r in result]
Beispiel #3
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 def get_enrollment(self, study, ind_label):
   query = """select e
   from Enrollment e join fetch e.study as s
   where e.studyCode = :ilabel and s.id = :sid
   """
   pars = self.kb.ome_query_params({
     'ilabel': wp.ome_wrap(ind_label),
     'sid': wp.ome_wrap(study.omero_id),
     })
   result = self.kb.ome_operation("getQueryService", "findByQuery",
                                  query, pars)
   return None if result is None else self.kb.factory.wrap(result)
Beispiel #4
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 def get_vessels_collection(self, label):
   """
   Return the VesselsCollection object labeled 'label' or None if
   nothing matches 'label'.
   """
   query = 'select vc from VesselsCollection vc where vc.label = :label'
   pars = self.kb.ome_query_params({'label' : wp.ome_wrap(label, wp.STRING)})
   result = self.kb.ome_operation('getQueryService', 'findByQuery',
                                  query, pars)
   return None if result is None else self.kb.factory.wrap(result)
Beispiel #5
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 def get_data_collection(self, label):
   """
   Return the DataCollection object labeled 'label' or
   None if nothing matches 'label'.
   """
   query = 'select dc from DataCollection dc where dc.label = :label'
   pars = self.kb.ome_query_params({'label': wp.ome_wrap(label, wp.STRING)})
   result = self.kb.ome_operation("getQueryService", "findByQuery",
                                  query, pars)
   return None if result is None else self.kb.factory.wrap(result)
Beispiel #6
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 def get_study(self, label):
   """
   Return the Study object labeled 'label' or None if nothing
   matches 'label'.
   """
   query = 'select st from Study st where st.label = :label'
   pars = self.kb.ome_query_params({'label': wp.ome_wrap(label, wp.STRING)})
   result = self.kb.ome_operation("getQueryService", "findByQuery",
                                  query, pars)
   return None if result is None else self.kb.factory.wrap(result)
Beispiel #7
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 def get_container(self, label):
   assert isinstance(label, str)
   query = """select c
   from Container c
   where c.label = :label
   """
   pars = self.kb.ome_query_params({'label': wp.ome_wrap(label)})
   result = self.kb.ome_operation("getQueryService", "findByQuery",
                                  query, pars)
   return None if result is None else self.kb.factory.wrap(result)
Beispiel #8
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 def get_data_objects(self, sample):
   query = """select do
   from DataObject do
   join fetch do.sample as s
   where s.id  = :sid
   """
   pars = self.kb.ome_query_params({
     'sid': wp.ome_wrap(sample.omero_id, wp.LONG),
     })
   result = self.kb.ome_operation("getQueryService", "findAllByQuery",
                                  query, pars)
   return [self.kb.factory.wrap(i) for i in result]
Beispiel #9
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 def get_vessels_collection_items(self, vc):
   query = """select i
   from VesselsCollectionItem i
   join fetch i.vessel as v
   join fetch i.vesselsCollection as vc
   where vc.id = :vcid
   """
   pars = self.kb.ome_query_params({
       'vcid' : wp.ome_wrap(vc.omero_id, wp.LONG),
       })
   result = self.kb.ome_operation('getQueryService', 'findAllByQuery',
                                  query, pars)
   return [self.kb.factory.wrap(i) for i in result]
Beispiel #10
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 def get_data_collection_items(self, dc):
   query = """select i
   from DataCollectionItem i
   join fetch i.dataSample as s
   join fetch i.dataCollection as dc
   where dc.id  = :dcid
   """
   pars = self.kb.ome_query_params({
     'dcid': wp.ome_wrap(dc.omero_id, wp.LONG),
     })
   result = self.kb.ome_operation("getQueryService", "findAllByQuery",
                                  query, pars)
   return [self.kb.factory.wrap(i) for i in result]
Beispiel #11
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 def get_enrolled(self, study):
   query = """select e
   from Enrollment e
   join fetch e.study as s
   join fetch e.individual as i
   where s.label = :slabel
   """
   pars = self.kb.ome_query_params({
     'slabel': wp.ome_wrap(study.label, wp.STRING),
     })
   result = self.kb.ome_operation("getQueryService", "findAllByQuery",
                                  query, pars)
   return [self.kb.factory.wrap(e) for e in result]
Beispiel #12
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 def get_snp_markers_set(self, label, maker, model, release):
   if label:
     query = """select ms
     from SNPMarkersSet ms
     where ms.label = :label
     """
     pars = self.kb.ome_query_params({'label': wp.ome_wrap(label)})
   else:
     if not (maker and model and release):
       raise ValueError('maker model and release should be all provided')
     query = """select ms
     from SNPMarkersSet ms
     where ms.maker = :maker
     and ms.model = :model
     and ms.release = :release
     """
     pars = self.kb.ome_query_params({
       'maker': wp.ome_wrap(maker),
       'model': wp.ome_wrap(model),
       'release': wp.ome_wrap(release),
       })
   result = self.kb.ome_operation("getQueryService", "findByQuery",
                                  query, pars)
   return None if result is None else self.kb.factory.wrap(result)
Beispiel #13
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 def get_vessels(self, klass, content):
   if not issubclass(klass, self.kb.Vessel):
     raise ValueError('klass should be a subclass of Vessel')
   if not content:
     query = "select v from %s v" % klass.get_ome_table()
     pars = None
   elif isinstance(content, self.kb.VesselContent):
     value = content.ome_obj.value._val
     query = """select v from %s v join fetch v.content as c
     where c.value = :cvalue
     """ % klass.get_ome_table()
     pars = self.kb.ome_query_params({'cvalue': wp.ome_wrap(value)})
   else:
     raise ValueError('content should be an instance of VesselContent')
   results = self.kb.ome_operation('getQueryService', 'findAllByQuery',
                                   query, pars)
   return [self.kb.factory.wrap(v) for v in results]