Merge pull request #126 from plantbreeding/issue-107

made all parameter datatypes consistent

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)
 

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)
 
         { 

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)
 

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)
 

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)
 

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)
 

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)

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)
 

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)
 
         {

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)
 
         {

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.

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)
 

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)
 

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)