def post(self, request, format=None, *args, **kwargs):
queryset = Germplasm.objects.all()
# PARAMS:
# {
# "germplasmPUIs" : [ "http://www.crop-diversity.org/mgis/accession/01BEL084609", "doi:10.15454/328757862534E12" ],
# "germplasmDbIds" : [ "986", "01BEL084609" ],
# "germplasmSpecies" : [ "aestivum", "vinifera" ],
# "germplasmGenus" : [ "Solanum", "Triticum" ],
# "germplasmNames" : [ "XYZ1", "Pahang" ],
# "accessionNumbers": [ "ITC0609", "ITC0685" ],
# "pageSize" : 100,
# "page": 1
# }
params = self.request.data
logger = logging.getLogger(__name__)
logger.warn("Parameters: %s" % params)
queryset = search_post_params_in(
self, queryset, [('germplasmNames', 'germplasmName'),
('germplasmDbId', 'germplasmDbId'),
('germplasmPUIs', 'germplasmPUI'),
('germplasmSpecies', 'germplasmSpecies'),
('germplasmGenus', 'germplasmGenus'),
('accessionNumbers', 'accessionNumber')])
return paginate(queryset, request, GermplasmSerializer)
def post(self, request, format=None, *args, **kwargs):
queryset = Program.objects.all()
# PARAMS:
# {
# "programDbId": "123",
# "name": "Wheat Resistance Program",
# "abbreviation" : "DRP1",
# "objective" : "Disease resistance",
# "leadPerson" : "Dr. Henry Beachell"
# }
params = self.request.data
logger = logging.getLogger(__name__)
logger.warn("Search parameters: %s" % params)
queryset = search_post_params_in(self, queryset,
[('programDbId', 'programDbId'),
('name', 'name'),
('abbreviation', 'abbreviation'),
('objective', 'objective'),
('leadPerson', 'leadPerson')], False)
return paginate(queryset, request, ProgramSerializer)
def get(self, request, format=None, *args, **kwargs):
mapDbId = self.kwargs['mapDbId']
queryset = Map.objects.all()
queryset = queryset.filter(mapDbId=mapDbId)
return paginate(queryset, request, MapDetailSerializer)
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 = 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 = Call.objects.all()
return paginate(queryset, request, CallsSerializer)
# end def get
# end class CallsView
def get(self, request, format=None, *args, **kwargs):
queryset = ObsVariable.objects.all()
observationVariableDbId = self.kwargs.get('observationVariableDbId', None)
if observationVariableDbId is not None:
queryset = queryset.filter(observationVariableDbId=observationVariableDbId)
# end if
return paginate(queryset, request, ObsVariableSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Marker.objects.all()
markerDbId = self.kwargs.get('markerDbId', None)
if markerDbId is not None:
queryset = queryset.filter(markerDbId=markerDbId)
# end if
return paginate(queryset, request, MarkerSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Germplasm.objects.all()
germplasmDbId = self.kwargs.get('germplasmDbId', None)
if germplasmDbId is not None:
queryset = queryset.filter(germplasmDbId=germplasmDbId)
# end if
return paginate(queryset, request, GermplasmSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = StudyPlot.objects.all()
studyDbId = self.kwargs.get('studyDbId', None)
if studyDbId is not None:
queryset = queryset.filter(studyDbId=studyDbId)
# end if
return paginate(queryset, request, StudyPlotSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = Trait.objects.all()
traitDbId = self.kwargs.get('traitDbId', None)
if traitDbId is not None:
queryset = queryset.filter(traitDbId=traitDbId)
# end if
return paginate(queryset, request, TraitSerializer)
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 = ObsVariable.objects.all()
# this search is not standard since it is on a related table
param_value = self.request.query_params.get('traitClass', None)
if param_value is not None:
queryset = queryset.filter(trait__classe=param_value)
# end if
return paginate(queryset, request, ObsVariableSerializer)
def post(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_post_params_in(
self, queryset, [('markerprofileDbId', 'markerprofileDbId'),
('markerDbId', 'markerDbId')])
return paginate(queryset, request, AlleleMSearchSerializer,
BrAPIListPagination)
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):
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 = Sample.objects.all()
sampleId = self.kwargs.get('sampleId', None)
logger = logging.getLogger(__name__)
logger.warn("Sample id '%s'" % sampleId)
if sampleId is not None:
queryset = queryset.filter(sampleId=sampleId)
# end if
return paginate(queryset, request, SampleSerializer)
def post(self, request, format=None, *args, **kwargs):
queryset = Study.objects.all()
queryset = search_post_params_in(
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):
queryset = Location.objects.all()
locationDbId = self.kwargs.get('locationDbId', None)
if locationDbId is not None:
queryset = queryset.filter(locationDbId=locationDbId)
# end if
return paginate(queryset, request, LocationSerializer)
# end def get
# end class LocationDetailsView
def get(self, request, format=None, *args, **kwargs):
queryset = GermplasmMarkerprofile.objects.all()
germplasmDbId = self.kwargs.get('id', None)
if germplasmDbId is not None:
queryset = queryset.filter(germplasmDbId=germplasmDbId)
# end if
return paginate(queryset, request, GermplasmMarkerprofileSerializer)
# end def get
# end class GermplasmMarkerprofileView
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 = GPPedigree.objects.all()
germplasmDbId = self.kwargs.get('germplasmDbId', None)
if germplasmDbId is not None:
queryset = queryset.filter(germplasmDbId=germplasmDbId)
# end if
notation = self.request.query_params.get('notation', None)
if notation is not None:
raise Exception('Deal with "notation" parameter')
# end if
return paginate(queryset, request, GPPedigreeSerializer)
def post(self, request, format=None, *args, **kwargs):
params = self.request.data
logger = logging.getLogger(__name__)
logger.warn("Search parameters: %s" % params)
queryset = ObsVariable.objects.all()
# TODO: add ('datatypes'), ('traitClasses')
queryset = search_post_params_in(self, queryset, [('observationVariableDbId', 'observationVariableDbIds'),
('ontologyXref', 'ontologyXrefs'),
('ontologyDbId', 'ontologyDbIds'),
('method', 'methodDbIds'),
('scale', 'scaleDbIds'),
('name', 'names')])
return paginate(queryset, request, ObsVariableSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = MarkerProfile.objects.all()
markerprofileDbId = self.kwargs.get('markerprofileDbId', None)
logger = logging.getLogger(__name__)
logger.warn("Markerprofiles data: %s" % markerprofileDbId)
if markerprofileDbId is not None:
queryset = queryset.filter(
markerProfilesDbId_details=markerprofileDbId)
# end if
# TODO: it is not clear to which data the query parameters apply!
# unknownString=&sepPhased=&sepUnphased=&expandHomozygotes=
return paginate(queryset, request, MarkerProfileSerializer)
def get(self, request, format=None, *args, **kwargs):
queryset = GermplasmAttr.objects.all()
germplasmDbId = self.kwargs.get('germplasmDbId', None)
if germplasmDbId is not None:
queryset = queryset.filter(germplasmDbId=germplasmDbId)
# end if
attributeDbIds = self.request.query_params.get('attributeList', None)
logger = logging.getLogger(__name__)
logger.warn("FILTERING: %s (IN %s)" % (germplasmDbId, attributeDbIds))
if attributeDbIds is not None:
queryset = queryset.filter(attributeDbId__in=attributeDbIds)
# end if
return paginate(queryset, request, GermplasmAttrSerializer)
def post(self, request, format=None, *args, **kwargs):
queryset = Phenotype.objects.all()
# PARAMS:
# {
# "germplasmDbIds" : [ "Blabla", "34Mtp362" ], // (optional, text, `986`) ... The name or synonym of external genebank accession identifiers
# "observationVariableDbIds" : [ "37373", "CO_321:00000234"], // (optional, text, `CO_321:00000234`) ... The IDs of traits, could be ontology ID, database ID or PUI
# "studyDbIds" : [ "383", "2929", "WHEAT_NETWK_2016_MONTPELLIER" ], // (optional, text, `2356`) ... The database ID / PK of the studies search parameter
# "locationDbIds" : [ "383838", "MONTPELLIER" ], // locations these traits were collected
# "programDbIds" : [ "3838", "Drought resistance CG 2020" ], // list of programs that have phenotyped this trait
# "seasonDbIds" : [ "338", "2010", "1956-2014", "2002-2003-2004", "2007 Spring" ], // (optional, text, `2001`) ... The year or Phenotyping campaign of a multiannual study (trees, grape, ...)
# "observationLevel" : "plot", // (optional, text, `plot`) ... The type of the observationUnit. Returns only the observaton unit of the specified type; the parent levels ID can be accessed through observationUnitStructure.
# "observationTimeStampRange" : ["2015-06-16T00:53:26-0800","2015-06-18T00:53:26-0800"]
# "pageSize" : 100, // (optional, integer, `1000`) ... The size of the pages to be returned. Default is `1000`.
# "page" : 1, // (optional, integer, `10`) ... Which result page is requested
# }
params = self.request.data
logger = logging.getLogger(__name__)
logger.warn("Search parameters: %s" % params)
queryset = search_post_params_in(
self, queryset,
[('germplasmDbIds', 'germplasmDbIds'),
('observationVariableDbIds', 'observationVariableDbIds'),
('studyDbIds', 'studyDbIds'), ('locationDbIds', 'locationDbIds'),
('programDbIds', 'programDbIds'), ('seasonDbIds', 'seasonDbIds'),
('observationLevel', 'observationLevel')])
observationTimeStampRange = params.get('observationTimeStampRange',
None)
if observationTimeStampRange is not None:
queryset = queryset.filter(
Q(observationTimeStampRange__gte=observationTimeStampRange[0])
&
Q(observationTimeStampRange__lte=observationTimeStampRange[1]))
# end if
#serializer = PhenotypeSerializer(queryset, many=True)
return paginate(queryset, request, PhenotypeSerializer)
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(self, request, format=None, *args, **kwargs):
logger = logging.getLogger(__name__)
mapDbId = self.kwargs['mapDbId']
queryset = MapLinkage.objects.all()
linkageGroupId = self.kwargs['linkageGroupId']
logger.warn("Positions: (%s, %s)" % (mapDbId, linkageGroupId))
queryset = queryset.filter(Q(mapDbId=mapDbId)&Q(linkageGroupId=linkageGroupId))
# numerical filters, therefore cannot use '_search_get_qparams'
min_pos = self.request.query_params.get('min', None)
if min_pos is not None:
queryset = queryset.filter(location__gte=min_pos)
# end if
max_pos = self.request.query_params.get('max', None)
if max_pos is not None:
queryset = queryset.filter(location__lte=max_pos)
# end if
return paginate(queryset, request, MapLinkageSerializer)
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)
def get(self, request, format=None, *args, **kwargs):
queryset = Trait.objects.all()
return paginate(queryset, request, TraitSerializer)
