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Merge pull request #241 from plantbreeding/issue-191
Issue 191
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| Original file line number | Diff line number | Diff line change |
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| ### Phenotypes Search (CSV) [POST /brapi/v1/phenotypes-search/csv] | ||
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| + Request (application/json) | ||
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| { | ||
| "germplasmDbIds" : [ "Blabla", "34Mtp362" ], // (optional) The name or synonym of external genebank accession identifiers | ||
| "observationVariableDbIds" : [ "37373", "CO_321:00000234"], // (optional) The IDs of traits, could be ontology ID, database ID or PUI | ||
| "studyDbIds" : [ "383", "2929", "WHEAT_NETWK_2016_MONTPELLIER" ], // (optional) The database ID / PK of the studies search parameter | ||
| "locationDbIds" : [ "383838", "MONTPELLIER" ], // (optional) locations these traits were collected | ||
| "trialDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of trials to search across | ||
| "programDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of programs to search across | ||
| "seasonDbIds" : [ "338", "2010", "1956-2014", "2002-2003-2004", "2007 Spring" ], // (optional) The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) | ||
| "observationLevel" : "plot", // (optional) The type of the observationUnit. Returns only the observation unit of the specified type; the parent levels ID can be accessed through observationUnitStructure. | ||
| "observationTimeStampRangeStart" : "2015-06-16T00:53:26-0800" // (optional) Timestamp range start | ||
| "observationTimeStampRangeEnd" : "2015-06-18T00:53:26-0800" // (optional) Timestamp range end | ||
| "pageSize" : 100, // (optional) The size of the pages to be returned. Default is `1000`. | ||
| "page" : 0, // (optional) Which result page is requested | ||
| } | ||
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| + Response 200 (application/csv) | ||
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| "year","studyDbId","studyName","locationDbId","locationName","germplasmDbId","germplasmName","observationUnitDbId","plotNumber","replicate","blockNumber", "entryType", "X", "Y", "variableDbId1", "variableDbId2", "variableDbId3" | ||
| "2015", "YieldStudy2015-5", "Yield wheat 2015", "mtp-north-32", "Montpellier", "doi:10.155454/12349537E12", "IR-8", "2016-Maugio-34-575-abc-123", "120", "", "2", "", "5", "15", "45", "3", "10" | ||
| "2016", "YieldStudy2016-5", "Yield wheat 2016", "mtp-north-32", "Montpellier", "doi:10.155454/12349537E13", "IR-8", "2016-Maugio-34-575-abc-124", "120", "", "2", "", "5", "15", "47", "4", "11" | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,132 @@ | ||
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| ### Phenotype Search (POST) [POST /brapi/v1/phenotypes-search] | ||
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| + Request (application/json) | ||
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| { | ||
| "germplasmDbIds" : [ "Blabla", "34Mtp362" ], // (optional) The name or synonym of external genebank accession identifiers | ||
| "observationVariableDbIds" : [ "37373", "CO_321:00000234"], // (optional) The IDs of traits, could be ontology ID, database ID or PUI | ||
| "studyDbIds" : [ "383", "2929", "WHEAT_NETWK_2016_MONTPELLIER" ], // (optional) The database ID / PK of the studies search parameter | ||
| "locationDbIds" : [ "383838", "MONTPELLIER" ], // (optional) locations these traits were collected | ||
| "trialDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of trials to search across | ||
| "programDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of programs that have phenotyped this trait | ||
| "seasonDbIds" : [ "338", "2010", "1956-2014", "2002-2003-2004", "2007 Spring" ], // (optional) The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) | ||
| "observationLevel" : "plot", // (optional) The type of the observationUnit. Returns only the observation unit of the specified type; the parent levels ID can be accessed through observationUnitStructure. | ||
| "observationTimeStampRangeStart" : "2015-06-16T00:53:26-0800" // (optional) Timestamp range start | ||
| "observationTimeStampRangeEnd" : "2015-06-18T00:53:26-0800" // (optional) Timestamp range end | ||
| "pageSize" : 100, // (optional) The size of the pages to be returned. Default is `1000`. | ||
| "page" : 1, // (optional) Which result page is requested | ||
| } | ||
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| + Response 200 (application/json) | ||
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| { | ||
| "metadata": { | ||
| "pagination": { | ||
| "pageSize": 100, | ||
| "currentPage": 1, | ||
| "totalCount": 102, | ||
| "totalPages": 2 | ||
| }, | ||
| "status": [], | ||
| "datafiles": [] | ||
| }, | ||
| "result": { | ||
| "data": [ | ||
| { | ||
| "observationUnitDbId": "2016-Maugio-34-575-abc-123", | ||
| "observationLevel": "plot", | ||
| "observationLevels": "bloc:2,subBloc:1,plot:2016-Maugio-34-575-abc-123", | ||
| "plotNumber": "2016-Maugio-34-575-abc-123", | ||
| "plantNumber" : null, | ||
| "blockNumber" : "2", | ||
| "replicate": null, | ||
| "observationUnitName": "2016-Maugio-34-575", | ||
| "germplasmDbId": "doi:10.155454/12349537E12", | ||
| "germplasmName": "IR-8", | ||
| "studyDbId": "YieldStudy2015-5", | ||
| "studyName": "Yield wheat 2015", | ||
| "studyLocationDbId": "mtp-north-32", | ||
| "studyLocation": "Montpellier", | ||
| "programName": "Whealbi", | ||
| "X": "5", | ||
| "Y": "15", | ||
| "entryType": null, | ||
| "entryNumber": null, | ||
| "treatments": [ | ||
| { | ||
| "factor": "water regimen", | ||
| "modality": "water deficit" | ||
| } | ||
| ], | ||
| "observationUnitXref":[ | ||
| {"source": "biosampleEBI", "id": "SAMEA179865230"}, | ||
| {"source": "gnpis.lot", "id": "INRA:CoeSt6 _SMH03"}, | ||
| {"source": "kernelDB", "id": "239865"} | ||
| ], | ||
| "observations": [ | ||
| { | ||
| "observationDbId": "153453453", | ||
| "observationVariableDbId": "CO_321:0000045", | ||
| "observationVariableName": "Plant_height", | ||
| "observationTimeStamp": "2015-06-16T00:53:26-0800", | ||
| "season": "2015", | ||
| "collector": "Mr. Technician", | ||
| "value": "45" | ||
| }, | ||
| { | ||
| "observationDbId": "23453454345", | ||
| "observationVariableDbId": "CO_321:0000996", | ||
| "observationVariableName": "GW100_g", | ||
| "observationTimeStamp": "2015-06-16T00:53:26-0800", | ||
| "season": "2015", | ||
| "collector": "Mr. Technician", | ||
| "value": "3" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "observationUnitDbId": "45204", | ||
| "observationLevel": "plant", | ||
| "observationLevels": null, | ||
| "plotNumber": null, | ||
| "plantNumber" : "45204", | ||
| "blockNumber" : null, | ||
| "replicate": "2", | ||
| "observationUnitName": "2010-Cornell-37-99", | ||
| "germplasmDbId": "doi:10.155499/12349537E00", | ||
| "germplasmName": "ZE-45", | ||
| "studyDbId": "YieldStudy2010-5", | ||
| "studyName": "Yield wheat 2010", | ||
| "studyLocationDbId": "88484", | ||
| "studyLocation": "Cornell", | ||
| "programName": "Wheat for futur", | ||
| "X": null, | ||
| "Y": null, | ||
| "entryType": null, | ||
| "entryNumber": null, | ||
| "treatments": [], | ||
| "observations": [ | ||
| { | ||
| "observationDbId": "153453453", | ||
| "observationVariableDbId": "CO_321:0000045", | ||
| "observationVariableName": "Plant_height", | ||
| "observationTimeStamp": "2010-06-16T00:53:26-0800", | ||
| "season": "2010", | ||
| "collector": "Mr. Technician", | ||
| "value": "45" | ||
| }, | ||
| { | ||
| "observationDbId": "23453454345", | ||
| "observationVariableDbId": "CO_321:0000996", | ||
| "observationVariableName": "GW100_g", | ||
| "observationTimeStamp": "2010-06-16T00:53:26-0800", | ||
| "season": "2010", | ||
| "collector": "Mr. Technician", | ||
| "value": "3" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
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| ### Phenotypes Search (TSV) [POST /brapi/v1/phenotypes-search/tsv] | ||
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| + Request (application/json) | ||
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| { | ||
| "germplasmDbIds" : [ "Blabla", "34Mtp362" ], // (optional) The name or synonym of external genebank accession identifiers | ||
| "observationVariableDbIds" : [ "37373", "CO_321:00000234"], // (optional) The IDs of traits, could be ontology ID, database ID or PUI | ||
| "studyDbIds" : [ "383", "2929", "WHEAT_NETWK_2016_MONTPELLIER" ], // (optional) The database ID / PK of the studies search parameter | ||
| "locationDbIds" : [ "383838", "MONTPELLIER" ], // (optional) locations these traits were collected | ||
| "trialDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of trials to search across | ||
| "programDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of programs to search across | ||
| "seasonDbIds" : [ "338", "2010", "1956-2014", "2002-2003-2004", "2007 Spring" ], // (optional) The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) | ||
| "observationLevel" : "plot", // (optional) The type of the observationUnit. Returns only the observation unit of the specified type; the parent levels ID can be accessed through observationUnit Structure. | ||
| "observationTimeStampRangeStart" : "2015-06-16T00:53:26-0800" // (optional) Timestamp range start | ||
| "observationTimeStampRangeEnd" : "2015-06-18T00:53:26-0800" // (optional) Timestamp range end | ||
| "pageSize" : 100, // (optional) The size of the pages to be returned. Default is `1000`. | ||
| "page" : 1, // (optional) Which result page is requested | ||
| } | ||
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| + Response 200 (application/tsv) | ||
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| "year" "studyDbId" "studyName" "locationDbId" "locationName" "germplasmDbId" "germplasmName" "observationUnitDbId" "plotNumber" "replicate" "blockNumber" "entryType" "X" "Y" "variableDbId1" "variableDbId2" "variableDbId3" | ||
| "2015" "YieldStudy2015-5" "Yield wheat 2015" "mtp-north-32" "Montpellier" "doi:10.155454/12349537E12" "IR-8" "2016-Maugio-34-575-abc-123" "120" "" "2" "" "5" "15" "45" "3" "10" | ||
| "2016" "YieldStudy2016-5" "Yield wheat 2016" "mtp-north-32" "Montpellier" "doi:10.155454/12349537E13" "IR-8" "2016-Maugio-34-575-abc-124" "120" "" "2" "" "5" "15" "47" "4" "11" | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
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| ### Phenotypes Search (Table) [POST /brapi/v1/phenotypes-search/table] | ||
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| + Request (application/json) | ||
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| { | ||
| "germplasmDbIds" : [ "Blabla", "34Mtp362" ], // (optional) The name or synonym of external genebank accession identifiers | ||
| "observationVariableDbIds" : [ "37373", "CO_321:00000234"], // (optional) The IDs of traits, could be ontology ID, database ID or PUI | ||
| "studyDbIds" : [ "383", "2929", "WHEAT_NETWK_2016_MONTPELLIER" ], // (optional) The database ID / PK of the studies search parameter | ||
| "locationDbIds" : [ "383838", "MONTPELLIER" ], // (optional) locations these traits were collected | ||
| "trialDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of trials to search across | ||
| "programDbIds" : [ "3838", "Drought_resistance_CG_2020" ], // (optional) list of programs to search across | ||
| "seasonDbIds" : [ "338", "2010", "1956-2014", "2002-2003-2004", "2007 Spring" ], // (optional) The year or Phenotyping campaign of a multi-annual study (trees, grape, ...) | ||
| "observationLevel" : "plot", // (optional) The type of the observationUnit. Returns only the observation unit of the specified type; the parent levels ID can be accessed through observationUnit Structure. | ||
| "observationTimeStampRangeStart" : "2015-06-16T00:53:26-0800" // (optional) Timestamp range start | ||
| "observationTimeStampRangeEnd" : "2015-06-18T00:53:26-0800" // (optional) Timestamp range end | ||
| "pageSize" : 100, // (optional) The size of the pages to be returned. Default is `1000`. | ||
| "page" : 0, // (optional) Which result page is requested | ||
| } | ||
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| + Response 200 (application/json) | ||
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| { | ||
| "metadata": { | ||
| "pagination": { | ||
| "pageSize": 100, | ||
| "currentPage": 0, | ||
| "totalCount": 2, | ||
| "totalPages": 1 | ||
| }, | ||
| "status": [], | ||
| "datafiles": [] | ||
| }, | ||
| "result" : { | ||
| "headerRow": [ "year","studyDbId","studyName","locationDbId","locationName","germplasmDbId","germplasmName","observationUnitDbId","plotNumber","replicate","blockNumber", "observationTimestamp", "entryType", "X", "Y"], | ||
| "observationVariableDbIds": [ "variable1DbId", "variable2DbId", "variable3DbId"], // for linking | ||
| "observationVariableNames": [ "plant height", "fruit weight", "root weight" ], // for display | ||
| // the observationNames will follow the columns defined in the headerRow | ||
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| "data" : | ||
| [ | ||
| ["2017", "stu1", "Study Name", "loc1", "Location Name", "CIP1", "CIP Name", "abc123", 1, 1, 1, "2017-06-16T00:53:26Z", "Test Entry", "1", "2", "25.3", "103.4", "50.75"], | ||
| ["2017", "stu1", "Study Name", "loc1", "Location Name", "CIP1", "CIP Name", "abc124", 1, 1, 1, "2017-06-16T00:54:57Z", "Test Entry", "2", "2", "27.9", "98.65", "45.345"] | ||
| ] | ||
| } | ||
| } | ||
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