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 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 = 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 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 post(self, request, format=None, *args, **kwargs):
params = self.request.data
logger = logging.getLogger(__name__)
logger.warn("Searching with parameters: %s" % params)
queryset = MarkerProfile.objects.all()
queryset = search_post_params_in(self, queryset,
[('germplasmDbId', 'germplasm'),
('studyDbId', 'studyDbId'),
('sampleDbId', 'sample'),
('extractDbId', 'extract'),
('analysisMethod', 'method')])
return paginate(queryset, request, MarkerProfileSerializer)
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 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)