def test_get_trial_details(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"trialDbId": 1,
"trialName": "Peru Yield Trial",
"programDbId": 1,
"name": "CIPHQ",
"startDate": "2013-01-01",
"endDate": "2013-07-05",
"active": false,
"studies": []
}
]
}
}"""
test_get(self, '/brapi/v1/trials/1', expected)
def test_get_types(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageSize": 100,
"totalCount": 3,
"pageTotal": 1
},
"datafiles": [],
"status": []
},
"result": {
"data": [
{
"name": "Crossing Nursery",
"description": "Description for Nursery study type"
},
{
"name": "Yield Trial",
"description": "Description for Trial study type"
},
{
"name": "Genotype",
"description": "Description for Genotyping study type"
}
]
}
}"""
test_get(self, '/brapi/v1/studyTypes/', expected)
def test_get_trait_details(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"traitDbId": 1,
"traitId": "CO_334:0100620",
"name": "Carotenoid content",
"description": "Cassava storage root pulp carotenoid content",
"observationVariables": [
"CO_334:0100621",
"CO_334:0100623",
"CO_334:0100623"
]
}
]
}
}"""
test_get(self, '/brapi/v1/traits/1', expected)
def test_get_programs(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 3,
"totalCount": 6,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"programDbId": 1,
"name": "CIPHQ",
"abbreviation": "CIPHQ",
"objective": "Global Population Improvement",
"leadPerson": "G. Leader"
},
{
"programDbId": 2,
"name": "Ghana",
"abbreviation": "GHA",
"objective": "OFSP",
"leadPerson": "M. Breeder"
}
]
}
}"""
test_get(self, '/brapi/v1/programs/?pageSize=2', expected)
def test_get_allele_matrices(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 2,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"name": "testDs1",
"matrixDbId": 27,
"description": "a test dataset",
"lastUpdated": "2017-06-12",
"studyDbId": 13
},
{
"name": "testDs2",
"matrixDbId": 28,
"description": "a second test dataset",
"lastUpdated": "2017-06-12",
"studyDbId": 13
}
]
}
}"""
test_get(self, '/brapi/v1/allelematrices/', expected)
def test_get_markerprofiles_data(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"markerProfilesDbId": 3,
"uniqueDisplayName": "germplasm3",
"sampleDbId": 33,
"extractDbId": 1,
"studyDbId": 1,
"analysisMethod": "GBS",
"resultCount": 1,
"germplasmDbId": 3
}
]
}
}"""
test_get(self, '/brapi/v1/markerprofiles/3/', expected)
def test_get_datatypes(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 6,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
"Numeric",
"Categorical",
"Date",
"Text",
"Picture",
"Boolean"
]
}
}"""
test_get(self, '/brapi/v1/variables/datatypes/', expected)
def test_get_obs_unit_details(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageSize": 100,
"totalCount": 1,
"pageTotal": 1
},
"datafiles": [],
"status": []
},
"result": {
"data": [
{
"studyDbId": 1,
"observationDbId": 3383838,
"observationUnitDbId": 11,
"observationUnitName": "ZIPA_68_Ibadan_2014",
"observationLevel": "plot",
"observationVariableDbId": 393939,
"observationVariableName": "Yield",
"observationTimestamp": "2015-11-05T14:12:56Z",
"uploadedBy": "dbUserId",
"operator": "Jane Doe",
"germplasmDbId": 8383,
"germplasmName": 143,
"value": 5
}
]
}
}"""
test_get(self, '/brapi/v1/studies/1/observationunits/', expected)
def test_get_seasons(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageSize": 2,
"totalCount": 10,
"pageTotal": 5
},
"datafiles": [],
"status": []
},
"result": {
"data": [
{
"seasonDbId": 1,
"season": "spring",
"year": 2011
},
{
"seasonDbId": 2,
"season": "summer",
"year": 2011
}
]
}
}"""
test_get(self, '/brapi/v1/seasons/?pageSize=2', expected)
def test_get_germplasm_attr_avail(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"attributeCategoryDbId": 1,
"code": "RHT",
"uri": "http://www.cropontology.org/rdf/CO_321:0000020",
"name": "Rht-B1b",
"description": "Allele of marker 11_4769, diagnostic for allele b of reduced-height gene Rht-B1''",
"datatype": "Categorical",
"values": [
"Present",
"Absent",
"Heterozygous"
]
}
]
}
}"""
test_get(self, '/brapi/v1/attributes/', expected)
def test_get_germplasm_attr_cats(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 2,
"totalCount": 3,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"attributeCategoryDbId": 1,
"name": "Morphological"
},
{
"attributeCategoryDbId": 2,
"name": "Agronomic"
}
]
}
}"""
test_get(self, '/brapi/v1/attributes/categories/?pageSize=2', expected)
def test_get_map_data_by_range(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 2,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"markerDbId": 1,
"markerName": "m1",
"location": 10,
"linkageGroupId": 1
},
{
"markerDbId": 2,
"markerName": "m2",
"location": 20,
"linkageGroupId": 1
}
]
}
}"""
test_get(self, '/brapi/v1/maps/1/positions/1?min=10&max=20', expected)
def test_get_markers(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 3,
"totalCount": 5,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"markerDbId": 1,
"defaultDisplayName": "a_01_10001",
"type": "SNP",
"synonyms": [
"i_01_10001",
"popA_10001"
],
"refAlt": [
"A",
"T"
],
"analysisMethods": [
"illumina"
]
},
{
"markerDbId": 2,
"defaultDisplayName": "A_01_10002",
"type": "SNP",
"synonyms": [
"i_01_10001",
"popA_10002"
],
"refAlt": [
"G",
"C"
],
"analysisMethods": [
"illumina"
]
}
]
}
}"""
test_get(self, '/brapi/v1/markers/?pageSize=2', expected)
def test_get_trials(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 5,
"totalCount": 9,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"additionalInfo": {
"values": {
"donorName": "Donor1",
"specialProject": "Project1"
}
},
"trialDbId": 1,
"trialName": "Peru Yield Trial",
"programDbId": 1,
"name": "CIPHQ",
"startDate": "2013-01-01",
"endDate": "2013-07-05",
"active": false,
"studies": []
},
{
"additionalInfo": null,
"trialDbId": 2,
"trialName": "Peru Genotype Trial",
"programDbId": 1,
"name": "CIPHQ",
"startDate": "2014-06-01",
"endDate": "2015-01-15",
"active": false,
"studies": []
}
]
}
}"""
test_get(self, '/brapi/v1/trials/?pageSize=2', expected)
def test_get_location_details(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"latitude": -11.1275,
"countryName": "Peru",
"abbreviation": "CIPSRM-1",
"instituteName": "INRA - GDEC",
"longitude": -75.356389,
"altitude": "828",
"instituteAdress": "route foo, Clermont Ferrand, France",
"locationType": "Storage location",
"additionalInfo": {
"values": {
" local": "San Ramon",
"crops": "potato,sweetpotato",
"cont": "South America",
"creg": "LAC",
"adm3": "San Ramon",
"adm2": "Chanchamayo",
"adm1": "Junin",
"annualTotalPrecipitation": "360",
"annualMeanTemperature": "23"
}
},
"locationDbId": 1,
"countryCode": "PER",
"name": "Experimental station San Ramon (CIP)"
}
]
}
}"""
test_get(self, '/brapi/v1/locations/1/', expected)
def test_get_plot_layout_details(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageSize": 2,
"totalCount": 6,
"pageTotal": 3
},
"datafiles": [],
"status": []
},
"result": {
"data": [
{
"studyDbId": 1,
"observationUnitDbId": 10001,
"observationUnitName": "ZIPA_68_Ibadan_2014",
"observationLevel": "plot",
"replicate": 1,
"germplasmDbId": 101,
"germplasmName": "ZIPA_68",
"blockNumber": 1,
"X": 1,
"Y": 1,
"entryType": "test"
},
{
"studyDbId": 1,
"observationUnitDbId": 10002,
"observationUnitName": "ZIPA_69_Ibadan_2014",
"observationLevel": "plot",
"replicate": 1,
"germplasmDbId": 102,
"germplasmName": "ZIPA_69",
"blockNumber": 1,
"X": 2,
"Y": 1,
"entryType": "test"
}
]
}
}"""
test_get(self, '/brapi/v1/studies/1/layout/?pageSize=2', expected)
def test_get_map(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"mapDbId": 1,
"name": "SSR map 1",
"type": "Genetic",
"unit": "cM",
"linkageGroups": [
{
"linkageGroupId": 1,
"markerCount": 21,
"maxPosition": 50
},
{
"linkageGroupId": 2,
"markerCount": 12,
"maxPosition": 100
},
{
"linkageGroupId": 3,
"markerCount": 7,
"maxPosition": 90
}
]
}
]
}
}"""
test_get(self, '/brapi/v1/maps/1/', expected)
def test_get_germplasm_attrs(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 3,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"attributeDbId": 1,
"attributeName": "Morphological",
"attributeCode": "FLSHORG",
"value": "Present",
"dateDetermined": "2016-01-01"
},
{
"attributeDbId": 2,
"attributeName": "Agronomic",
"attributeCode": "RHT",
"value": "Absent",
"dateDetermined": "2016-01-01"
},
{
"attributeDbId": 3,
"attributeName": "Biotic stress",
"attributeCode": "WEV",
"value": "Present",
"dateDetermined": "2016-01-01"
}
]
}
}"""
test_get(self, '/brapi/v1/germplasm/1/attributes', expected)
def test_get_samples(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"studyDbId": "StudyId-123",
"locationDbId": "LocationId-123",
"plotId": "PlotId-123",
"plantId": "PlantID-123",
"sampleId": "Unique-Plant-SampleID",
"takenBy": "Mr. Technician",
"sampleTimestamp": "2016-07-27T13:43:22Z",
"sampleType": "TypeOfSample",
"tissueType": "TypeOfTissue",
"notes": "Cut from infected leaf",
"studyName": "Yield Trial A",
"season": "Summer",
"locationName": "Kenya",
"entryNumber": 11,
"plotNumber": 1,
"germplasmDbId": 15,
"plantingTimestamp": "2016-01-01T22:22:21Z",
"harvestTimestamp": "2016-06-30T22:33:23Z"
}
]
}
}"""
test_get(self, '/brapi/v1/samples/Unique-Plant-SampleID', expected)
def test_get_calls(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 25,
"totalCount": 50,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"call": "token",
"datatypes": [
"json",
"text"
],
"methods": [
"POST",
"DELETE"
]
},
{
"call": "calls",
"datatypes": [
"json"
],
"methods": [
"GET"
]
}
]
}
}"""
test_get(self, '/brapi/v1/calls?pageSize=2', expected)
def test_get_maps(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 2,
"totalCount": 3,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"mapDbId": 1,
"name": "SSR map 1",
"species": "Ipomoea batatas",
"type": "Genetic",
"unit": "cM",
"publishedDate": "2016-01-06",
"comments": "",
"linkageGroupCount": 10
},
{
"mapDbId": 2,
"name": "SSR map 2",
"species": "Ipomoea trifida",
"type": "Genetic",
"unit": "cM",
"publishedDate": "2016-11-15",
"comments": "none",
"linkageGroupCount": 10
}
]
}
}"""
test_get(self, '/brapi/v1/maps/?pageSize=2', expected)
def test_get_allele_matrix_search(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 4,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
[
"1",
"1",
"A/B"
],
[
"1",
"2",
"B"
],
[
"2",
"1",
"A"
],
[
"2",
"2",
"A/B"
]
]
}
}"""
test_get(self, '/brapi/v1/allelematrix-search', expected)
def test_get_obs_levels(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageSize": 100,
"totalCount": 2,
"pageTotal": 1
},
"datafiles": [],
"status": []
},
"result": {
"data": [
"plant",
"plot"
]
}
}"""
test_get(self, '/brapi/v1/observationLevels/', expected)
def test_get_crops(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 2,
"totalCount": 4,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
"cassava",
"potato"
]
}
}"""
test_get(self, '/brapi/v1/crops/?pageSize=2', expected)
def test_get_ontologies(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 3,
"totalCount": 5,
"pageSize": 2
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"ontologyDbId": "CO_334",
"ontologyName": "Wheat ontology",
"authors": "J. Snow, H. Peterson",
"version": "v1.2",
"copyright": "2016, INRA",
"licence": "CC BY-SA 4.0"
},
{
"ontologyDbId": "CO_334",
"ontologyName": "Wheat ontology",
"authors": "J. Snow, H. Peterson",
"version": "v1.2",
"copyright": "2016, INRA",
"licence": "CC BY-SA 4.0"
}
]
}
}"""
test_get(self, '/brapi/v1/ontologies/?pageSize=2', expected)
def test_get_variable_details(self):
expected = """
{
"metadata": {
"pagination": {
"currentPage": 1,
"pageTotal": 1,
"totalCount": 1,
"pageSize": 100
},
"status": [],
"datafiles": []
},
"result": {
"data": [
{
"method": {
"methodDbId": "CO_334:0010320",
"name": "Visual Rating:total carotenoid by chart_method",
"classe": "Estimation",
"description": "Assessment of the level of yellowness in cassava storage root pulp using the tc chart",
"formula": "",
"reference": ""
},
"trait": {
"traitDbId": "CO_334:0100620",
"name": "Carotenoid content",
"classe": "physiological trait",
"description": "Cassava storage root pulp carotenoid content",
"synonyms": "carotenoid content measure",
"mainAbbreviation": "CC",
"alternativeAbbreviations": "CCS",
"entity": "root",
"attribute": "carotenoid",
"status": "recommended",
"xref": "TL_455:0003023",
"uniqueDisplayName": "",
"extractDbId": null,
"markerprofileDbId": null,
"analysisMethod": "",
"data": ""
},
"scale": {
"validValues": {
"categories": [
"1"
],
"min": 2,
"max": 2
},
"scaleDbId": "CO_334:0100526",
"name": "ug/g",
"datatype": "Numeric",
"decimalPlaces": "0",
"xref": null
},
"observationVariableDbId": "CO_334:0100622",
"name": "caro_spectro",
"ontologyDbId": "CO_334",
"ontologyName": "Cassava",
"synonyms": "Carotenoid content by spectro",
"contextOfUse": "Trial evaluation; Nursery evaluation",
"growthStage": "mature",
"status": "recommended",
"xref": "TL_455:0003001",
"institution": null,
"scientist": null,
"date": "2016-05-13",
"language": "EN",
"crop": "cassava",
"defaultValue": "2"
}
]
}
}"""
test_get(self, '/brapi/v1/variables/CO_334:0100622/', expected)
