def get_queryset(self):
queryset = Program.objects.all()
return search_get_qparams(self, queryset,
[('programName', 'programName'),
('abbreviation', 'abbreviation')])
def get(self, request, format=None, *args, **kwargs):
queryset = StudyObsUnit.objects.all()
queryset = search_get_qparams(
self, queryset,
[('observationVariableDbIds', 'observationVariableDbIds')])
return paginate(queryset, request, StudyObsUnitSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Location.objects.all()
queryset = search_get_qparams(self, queryset,
[('locationType', 'locationType')])
return paginate(queryset, request, LocationSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Marker.objects.all()
# name, matchMethod, include
# possible values are 'case_insensitive', 'exact' (case sensitive), 'wildcard' (which is case insensitive). Wildcard uses both '*' and '%' for any number of characters and '?' for one character matching. Default is exact.
# Whether to include synonyms in the output.
name = self.request.query_params.get('name', None)
match_method = self.request.query_params.get('matchMethod', None)
include = self.request.query_params.get('include', None)
synonyms = include is not None and include == 'synonyms'
logger = logging.getLogger(__name__)
logger.warn("FILTERING: %s, method=%s, synonyms=%s" %
(name, match_method, synonyms))
if name is not None:
if match_method is not None:
if match_method == 'case_insensitive':
if synonyms:
queryset = queryset.filter(
Q(defaultDisplaydefaultDisplayName__iexact=name)
| Q(synonyms__iexact=name))
else:
queryset = queryset.filter(
defaultDisplayName__iexact=name)
# end if
elif match_method == 'wildcard':
# TODO: add prefixes and suffixes
name = name.replace('*', '')
name = name.replace('%', '')
if synonyms:
queryset = queryset.filter(
Q(defaultDisplayName__icontains=name)
| Q(synonyms__contains=name))
else:
queryset = queryset.filter(
defaultDisplayName__icontains=name)
# end if
# end if
else: # exact
if synonyms:
queryset = queryset.filter(
Q(defaultDisplayName=name) | Q(synonyms=name))
else:
queryset = queryset.filter(defaultDisplayName=name)
# end if
# end if
# end if
queryset = search_get_qparams(self, queryset, [('type', 'type')])
return paginate(queryset, request, MarkerSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = AlleleMSearch.objects.all()
# TODO: it is not clear to which data the query parameters apply!
# unknownString=&sepPhased=&sepUnphased=&expandHomozygotes=
queryset = search_get_qparams(
self, queryset, [('markerprofileDbId', 'markerprofileDbId'),
('markerDbId', 'markerDbId')])
return paginate(queryset, request, AlleleMSearchSerializer,
BrAPIListPagination)
def get(self, request, format=None, *args, **kwargs):
queryset = Germplasm.objects.all()
logger = logging.getLogger(__name__)
logger.warn("Searching with parameters %s" % self.request.query_params)
queryset = search_get_qparams(self, queryset,
[('germplasmName', 'germplasmName'),
('germplasmDbId', 'germplasmDbId'),
('germplasmPUI', 'germplasmPUI')])
return paginate(queryset, request, GermplasmSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Study.objects.all()
queryset = search_get_qparams(
self, queryset,
[('studyType', 'studyType'), ('seasonDbId', 'seasonDbId'),
('locationDbId', 'locationDbId'), ('programDbId', 'programDbId'),
('germplasmDbId', 'germplasmDbIds'),
('observationVariableDbId', 'observationVariableDbIds'),
('active', 'active')])
return paginate(queryset, request, StudySerializer)
def get(self, request, format=None, *args, **kwargs):
logger = logging.getLogger(__name__)
mapDbId = self.kwargs['mapDbId']
queryset = MapLinkage.objects.all()
linkageGroupId = self.request.query_params.get('linkageGroupId', None)
logger.warn("Linkages: (%s, %s)" % (mapDbId, linkageGroupId))
queryset = search_get_qparams(self, queryset, [('mapDbId', 'mapDbId'), ('linkageGroupId', 'linkageGroupId')])
return paginate(queryset, request, MapLinkageSerializer)
def get(self, request, format=None, *args, **kwargs):
logger = logging.getLogger(__name__)
logger.warn("Searching with parameters %s" % self.request.query_params)
queryset = MarkerProfile.objects.all()
queryset = search_get_qparams(self, queryset,
[('germplasmDbId', 'germplasm'),
('studyDbId', 'studyDbId'),
('sampleDbId', 'sample'),
('extractDbId', 'extract'),
('analysisMethod', 'method')])
return paginate(queryset, request, MarkerProfileSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Trial.objects.all()
queryset = search_get_qparams(self, queryset,
[('programDbId', 'programDbId'),
('locationDbId', 'locationDbId'),
('active', 'active')])
sortBy = self.request.query_params.get('sortBy', None)
sortOrder = self.request.query_params.get('sortOrder', None)
if sortBy is not None:
if sortOrder is not None and sortOrder == 'Ascending':
queryset = queryset.order_by(sortBy)
elif sortOrder is not None and sortOrder == 'Descending':
queryset = queryset.order_by('-' + sortBy)
# end if
# end if
return paginate(queryset, request, TrialSerializer)
def get_queryset(self):
queryset = StudySeason.objects.all()
return search_get_qparams(self, queryset, [('year', 'year')])
def get_queryset(self):
queryset = AlleleMatrix.objects.all()
return search_get_qparams(self, queryset, [('studyDbId', 'studyDbId')])
def get(self, request, format=None, *args, **kwargs):
queryset = Map.objects.all()
queryset = search_get_qparams(self, queryset, [('type', 'type'), ('species', 'species')])
return paginate(queryset, request, MapSerializer)