diff --git a/Specification/Germplasm/GermplasmDetailsByGermplasmDbId.md b/Specification/Germplasm/GermplasmDetailsByGermplasmDbId.md index 72dc96eb..5fb989eb 100644 --- a/Specification/Germplasm/GermplasmDetailsByGermplasmDbId.md +++ b/Specification/Germplasm/GermplasmDetailsByGermplasmDbId.md @@ -1,4 +1,4 @@ -## Germplasm Details by germplasmDbId [/brapi/v1/germplasm/{id}] +## Germplasm Details by germplasmDbId [/brapi/v1/germplasm/{germplasmDbId}] Scope: CORE. Status: ACCEPTED. Implementation target date: PAG2016 Implemented by: Tripal Brapi module, Germinate, Cassavabase @@ -37,7 +37,7 @@ Note: Germplasm Details by germplasmDbId was merged with Germplasm Multi Crop Pa ### Germplasm search by germplasmDbId [GET] + Parameters - + id (required, string, `382`) ... germplasmDbId - the internal id of the germplasm + + germplasmDbId (required, string, `382`) ... The internal id of the germplasm + Response 200 (application/json) diff --git a/Specification/Germplasm/GermplasmPedigree.md b/Specification/Germplasm/GermplasmPedigree.md index 3f60526f..f8c6ea47 100644 --- a/Specification/Germplasm/GermplasmPedigree.md +++ b/Specification/Germplasm/GermplasmPedigree.md @@ -1,4 +1,4 @@ -## Germplasm Pedigree [/brapi/v1/germplasm/{id}/pedigree?notation=purdy] +## Germplasm Pedigree [/brapi/v1/germplasm/{germplasmDbId}/pedigree?notation=purdy] Scope: CORE. Status: ACCEPTED. Implementation target date: PAG2016 Implemented by: Germinate, Tripal Brapi Module, Cassavabase (without notation option) @@ -18,8 +18,8 @@ Implemented by: Germinate, Tripal Brapi Module, Cassavabase (without notation op (http://wheat.pw.usda.gov/ggpages/gopher/administration/Template%20for%20Germplasm%20records.html) or [Lamacraft] (http://link.springer.com/article/10.1007%2FBF00021556). ### Germplasm pedigree by id [GET] + Parameters - + id (required, number, `382`) ... the internal id of the germplasm - + notation (optional, string, `purdy`) ... text representation of the pedigree + + germplasmDbId (required, string, `382`) ... the internal id of the germplasm + + notation (optional, string, `purdy`) ... text representation of the pedigree + Response 200 (application/json) { diff --git a/Specification/Germplasm/GermplasmSearchGET.md b/Specification/Germplasm/GermplasmSearchGET.md index 9972e5ee..14f921a9 100644 --- a/Specification/Germplasm/GermplasmSearchGET.md +++ b/Specification/Germplasm/GermplasmSearchGET.md @@ -46,11 +46,11 @@ Adresses these needs: Use GET when parameter size is less than 2K bytes. + Parameters - + germplasmPUI (optional, text, `http://data.inra.fr/accession/234Col342`) ... Permanent unique identifier (DOI, URI, etc.) - + germplasmDbId (optional, text, `986`) ... Internal database identifier - + germplasmName (optional, text, `Pah`, `Pahang`) ... Name of the germplasm - + pageSize (optional, integer, `1000`) ... The size of the pages to be returned. Default is `1000`. - + page (optional, integer, `10`) ... Which result page is requested + + germplasmPUI (optional, string, `http://data.inra.fr/accession/234Col342`) ... Permanent unique identifier (DOI, URI, etc.) + + germplasmDbId (optional, string, `986`) ... Internal database identifier + + germplasmName (optional, string, `Pah`, `Pahang`) ... Name of the germplasm + + pageSize (optional, integer, `1000`) ... The size of the pages to be returned. Default is `1000`. + + page (optional, integer, `10`) ... Which result page is requested + Response 200 (application/json) diff --git a/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md b/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md index 1fd4e43f..f18bd356 100644 --- a/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md +++ b/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md @@ -7,8 +7,8 @@ Values for all attributes by default. + Parameters + germplasmDbId (required, string, `993`) ... The germplasm characterized + attributeDbId (optional, string, `1`) ... Restrict the response to only the listed attributes. - + pageSize (optional, number, `10000`) ... the number of attributes to return in one request, defaults to 1000. - + page (optional, number, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + + pageSize (optional, integer, `10000`) ... the number of attributes to return in one request, defaults to 1000. + + page (optional, integer, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + Response 200 (application/json) diff --git a/Specification/GermplasmAttributes/ListAttributeCategories.md b/Specification/GermplasmAttributes/ListAttributeCategories.md index 506540e6..489baacb 100644 --- a/Specification/GermplasmAttributes/ListAttributeCategories.md +++ b/Specification/GermplasmAttributes/ListAttributeCategories.md @@ -5,8 +5,8 @@ Implementation target date: PAG2016 ### Germplasm attribute categories [GET] List all available attribute categories. + Parameters - + pageSize (optional, number, `10000`) Number of attributes to return in one response - + page (optional, number, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + + pageSize (optional, integer, `10000`) Number of attributes to return in one response + + page (optional, integer, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + Response 200 (application/json) diff --git a/Specification/Locations/ListLocations.md b/Specification/Locations/ListLocations.md index 64494fef..0c433ab8 100644 --- a/Specification/Locations/ListLocations.md +++ b/Specification/Locations/ListLocations.md @@ -13,8 +13,8 @@ Get a list of locations. + Parameters + locationType (optional, string, `Breeding Locations`) - Filter by location type specified. - + page (optional, int, `2282`) - request a specific response page - + pageSize (optional, int, `5000`) - request a non-default page size (1000 is default) + + page (optional, integer, `2282`) - request a specific response page + + pageSize (optional, integer, `5000`) - request a non-default page size (1000 is default) + Response 200 (application/json) diff --git a/Specification/MarkerProfiles/AlleleMatrices.md b/Specification/MarkerProfiles/AlleleMatrices.md index 29683ae6..f51a990a 100644 --- a/Specification/MarkerProfiles/AlleleMatrices.md +++ b/Specification/MarkerProfiles/AlleleMatrices.md @@ -12,7 +12,8 @@ This resource is used for reading and writing genomic matrices: ### Matrices through GET [GET] -+ Parameters: studyDbId restricts the list of matrices to a specific study. ++ Parameters + + studyDbId (required, string, `abc123`) ... restricts the list of matrices to a specific study. + Response 200 (application/json) diff --git a/Specification/MarkerProfiles/MarkerProfileData.md b/Specification/MarkerProfiles/MarkerProfileData.md index 242815fc..728ac982 100644 --- a/Specification/MarkerProfiles/MarkerProfileData.md +++ b/Specification/MarkerProfiles/MarkerProfileData.md @@ -36,13 +36,13 @@ Alphabetically? ### Alleles By Markerprofile Id [GET] + Parameters - + markerprofileDbId (required, number, `993`) ... The server's internal id for the markerprofile - + expandHomozygotes (optional, boolean, `false`) ... Should homozygotes NOT be collapsed into a single orrucance? - + unknownString (optional, string, `-`) ... The string to use as a representation for missing data or the reserved word "empty_string". - + sepPhased (optional, string, `|`) ... The string to use as a separator for phased allele calls or the reserved word "empty_string". - + sepUnphased (optional, string, `/`) ... The string to use as a separator for unphased allele calls or the reserved word "empty_string". - + pageSize (optional, number, `10000`) ... The number of allele call results (marker/allele pairs) to be returned in the response. If multiple experiments are requested, some responses will contain the last results from one experiment followed by the first results from the next. - + page (optional, number, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + + markerprofileDbId (required, String, `993`) ... The server's internal id for the markerprofile + + expandHomozygotes (optional, boolean, `false`) ... Should homozygotes NOT be collapsed into a single orrucance? + + unknownString (optional, string, `-`) ... The string to use as a representation for missing data or the reserved word "empty_string". + + sepPhased (optional, string, `|`) ... The string to use as a separator for phased allele calls or the reserved word "empty_string". + + sepUnphased (optional, string, `/`) ... The string to use as a separator for unphased allele calls or the reserved word "empty_string". + + pageSize (optional, integer, `10000`) ... The number of allele call results (marker/allele pairs) to be returned in the response. If multiple experiments are requested, some responses will contain the last results from one experiment followed by the first results from the next. + + page (optional, integer, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + Response 200 (application/json) diff --git a/Specification/MarkerProfiles/MarkerProfileSearch.md b/Specification/MarkerProfiles/MarkerProfileSearch.md index 0372b371..9687f7f2 100644 --- a/Specification/MarkerProfiles/MarkerProfileSearch.md +++ b/Specification/MarkerProfiles/MarkerProfileSearch.md @@ -15,8 +15,8 @@ For the requested Germplasm Id and/or Extract Id, returns the Markerprofile Id a + studyDbId (optional, string, `111`) ... The server's internal id for the StudyDbId + sampleDbId (optional, string, `184`) ... The server's internal id for the SampleDbId + extractDbId (optional, string, `84`) ... The server's internal id for the ExtractDbId - + pageSize (optional, number, `10000`) ... The number of allele call results (marker/allele pairs) to be returned in the response. If multiple experiments are requested, some responses will contain the last results from one experiment followed by the first results from the next. - + page (optional, number, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + + pageSize (optional, integer, `10000`) ... The number of allele call results (marker/allele pairs) to be returned in the response. If multiple experiments are requested, some responses will contain the last results from one experiment followed by the first results from the next. + + page (optional, integer, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + Response 200 (application/json) { diff --git a/Specification/MarkerProfiles/MarkerProfileSearchPost.md b/Specification/MarkerProfiles/MarkerProfileSearchPost.md index 284087a3..1d37de97 100644 --- a/Specification/MarkerProfiles/MarkerProfileSearchPost.md +++ b/Specification/MarkerProfiles/MarkerProfileSearchPost.md @@ -11,8 +11,8 @@ For the requested Germplasm Ids and/or Extract Ids, returns the Markerprofile Id + studyDbId (optional, string, `111`) ... The server's internal id for the StudyDbId + sampleDbId (optional, string, `184`) ... The server's internal id for the SampleDbId + extractDbId (optional, string, `84`) ... The server's internal id for the ExtractDbId - + pageSize (optional, number, `10000`) ... The number of allele call results (marker/allele pairs) to be returned in the response. If multiple experiments are requested, some responses will contain the last results from one experiment followed by the first results from the next. - + page (optional, number, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + + pageSize (optional, integer, `10000`) ... The number of allele call results (marker/allele pairs) to be returned in the response. If multiple experiments are requested, some responses will contain the last results from one experiment followed by the first results from the next. + + page (optional, integer, `1`) ... Required if `pageSize` is given; and requires that `pageSize` be given. The first page is 1, not 0. + Response 200 (application/json) { diff --git a/Specification/Markers/MarkerSearch.md b/Specification/Markers/MarkerSearch.md index bdacab7a..08e7279e 100644 --- a/Specification/Markers/MarkerSearch.md +++ b/Specification/Markers/MarkerSearch.md @@ -25,7 +25,7 @@ For the requested name or synonym, returns an array (possibly empty) of marker r ### Search names to retrieve marker records [GET] + Parameters - + name (optional, text, `11_10002 11_1% 11_1* 11_10?02`) ... The name or synonym. + + name (optional, string, `11_10002 11_1% 11_1* 11_10?02`) ... The name or synonym. + matchMethod (optional, string, `wildcard`) ... 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. diff --git a/Specification/Studies/GetObservationUnitsByObservationVariableIds.md b/Specification/Studies/GetObservationUnitsByObservationVariableIds.md index 622a819c..c94e298f 100644 --- a/Specification/Studies/GetObservationUnitsByObservationVariableIds.md +++ b/Specification/Studies/GetObservationUnitsByObservationVariableIds.md @@ -11,7 +11,7 @@ observationTimestamp should be ISO8601 format with timezone: YYYY-MM-DDThh:mm:ss + Parameters + studyDbId (required, string, `1`) ... Identifier of the study. Usually a number, could be alphanumeric. - + observationVariableDbId (required, number, `2` ... Numeric `id` of that variable (combination of trait, unit and method) + + observationVariableDbId (required, string, `2` ... Numeric `id` of that variable (combination of trait, unit and method) + Response 200 (application/json) diff --git a/Specification/Studies/ListStudySummaries.md b/Specification/Studies/ListStudySummaries.md index de05f64e..03fe41b1 100644 --- a/Specification/Studies/ListStudySummaries.md +++ b/Specification/Studies/ListStudySummaries.md @@ -24,8 +24,8 @@ StartDate and endDate should be ISO8601 format for dates: YYYY-MM-DD + germplasmDbIds (optional, array, `["CML123", "CML"]`) ... Filter studies where specified germplasm have been used/tested + observationVariableDbIds (optional, array, `["CO-PH-123" , "Var-123"]`) ... Filter studies where specified observation variables have been measured + active (optional, boolean, `true/false`) ... Filter active status true/false. - + sortBy (optional, boolean, `studyDbId`) ... Sort order. Name of the field to sorty by. - + sortOrder (optional, boolean, `asc/desc`) ... Sort order direction. Ascending/Descending. + + sortBy (optional, string, `studyDbId`) ... Sort order. Name of the field to sorty by. + + sortOrder (optional, string, `asc/desc`) ... Sort order direction. Ascending/Descending. + Response 200 (application/json) diff --git a/Specification/Trials/ListTrialSummaries.md b/Specification/Trials/ListTrialSummaries.md index 85e2b4b7..6238b012 100644 --- a/Specification/Trials/ListTrialSummaries.md +++ b/Specification/Trials/ListTrialSummaries.md @@ -29,8 +29,8 @@ Implementation target date: PAG2016. + pageSize (optional, integer, `1000`) + page (optional, integer, `100`) + active (optional, boolean, `true/false`) ... Filter active status true/false. - + sortBy (optional, boolean, `studyDbId`) ... Sort order. Name of the field to sorty by. - + sortOrder (optional, boolean, `asc/desc`) ... Sort order direction. Ascending/Descending. + + sortBy (optional, string, `studyDbId`) ... Sort order. Name of the field to sorty by. + + sortOrder (optional, string, `asc/desc`) ... Sort order direction. Ascending/Descending. + Response 200 (application/json)