Genesys API reference manual

December 2015: Documentation commit 69f33a84e9f4ce063877b1131e5709180be76dfc
version 2.3

All API access is over HTTPS, and accessed from the https://api.genesys-pgr.org domain or through https://api.sandbox.genesys-pgr.org for testing purposes. All data is sent and received as JSON. In this manual, all URLs are pointing to the Genesys sandbox environment at https://api.sandbox.genesys-pgr.org.

1. Security

Access to selected resources in Genesys is protected and user permissions are checked before any API action is executed. Each organization contributing data to Genesys will have one or more registered user accounts on Genesys.

To modify any data in Genesys, you will need appropriate permissions. Permission to access and manage data for the organization is granted by helpdesk@genesys-pgr.org upon request. Please contact helpdesk@genesys-pgr.org with the list of FAO WIEWS codes of institutes you wish to manage.

To access resources with the APIs described in this manual, you will first need to create a user account. The simplest way is to use your Google+ account, or alternatively to create an account manually.

Figure 1. Creating a user account

Access to the APIs is managed by the OAuth 2.0 protocol and implemented using spring-security OAuth modules. To obtain OAuth access and refresh tokens, you will first need a valid Client ID and Client Secret. These are generated by helpdesk@genesys-pgr.org for each individual consumer application. The ID and Secret listed below are valid for the Sandbox environment and allow out-of-band authentication when using curl in the examples in this manual.

Table 1. Client ID and Secret for out-of-band authentication
Client ID	`dLCiR.MzwkNha18ImEcw0ADli0@sandbox.genesys-pgr.org`
Client Secret	`wGmRAhVplWLEVWlqiMT712PMnaqOa8FN`

1.1. Obtaining the access token

Most OAuth libraries, including the genesys-client-api Java library, will automatically obtain the access token following the OAuth protocol. This section describes how to manually obtain the tokens.

1.1.1. Authorization grant

Obtain a verifier code by granting access to the "Genesys API reference" client. This is initiated by opening the authorization URL in a browser (please substitute CLIENTID and SECRET with valid data):

https://api.sandbox.genesys-pgr.org/oauth/authorize?client_id=CLIENTID&client_secret=SECRET&response_type=code&redirect_uri=oob&scope=write

The server will prompt you to authorize the access to your protected resources on Genesys. After your confirmation, the server will present an authorization code (which will look like: 7wXP1r). From a shell, execute the following curl command, with your authorization code in place of THECODE:

$ curl 'https://api.sandbox.genesys-pgr.org/oauth/token?grant_type=authorization_code&client_id=CLIENTID&client_secret=SECRET&redirect_uri=oob&code=THECODE'

1.1.2. Username and password

The password grant is available to trusted, secure clients (e.g. desktop applications) where the user’s password will not be captured or stored — i.e. it will be used once. A password grant can be used as follows:

$ curl 'https://api.sandbox.genesys-pgr.org/oauth/token' --data 'scope=write+read&grant_type=password&username=USERNAME&password=PASSWORD&client_id=CLIENT_ID&client_secret=CLIENT_SECRET'

1.1.3. Client credentials

System-to-system integration should not require user interaction. For that specific purpose, Genesys allows for an OAuth 2.0 client credentials grant.

With Genesys release 2.3, the client authentication grant is also supported. Kindly contact helpdesk@genesys-pgr.org for information on how to enable system-to-system integration and to grant your client the appropriate permissions on Genesys.

The client will be able to modify any data on Genesys on your behalf.

For more details, read the section "Client Credential Grant" in A Guide To OAuth 2.0 Grants.

To obtain a valid (but short-lived) access token, a simple POST request to Genesys is required:

$ curl -X POST 'https://api.sandbox.genesys-pgr.org/oauth/token?grant_type=client_credentials&client_id=CLIENTID&client_secret=SECRET&redirect_uri=oob'

This type of grant takes out the user authentication and authenticates the remote system with Genesys, immediately issuing an access token.

1.1.4. Successful authorization

The server will respond with access token details in JSON format:

{
        "access_token": "28d96a4e-9a31-479b-abc8-17ee1e8c9906",
        "token_type": "bearer",
        "refresh_token": "2583fd78-bd88-4c2b-afc0-fb231b37d95f",
        "expires_in": 43199,
        "scope": "read write"
}

You can use the access token to sign future HTTP requests to the API by adding a HTTP request header:

Authorization: Bearer OAUTH-ACCESS-TOKEN

as a curl parameter:

curl -H "Authorization: Bearer OAUTH-TOKEN" https://sandbox.genesys-pgr.org

or by including it in the request URL as a query string parameter:

$ curl 'https://api.sandbox.genesys-pgr.org/api/v0/me?access_token=OAUTH-ACCESS-TOKEN'

1.2. Using the refresh token

OAuth access tokens have a fairly short lifetime. When an access token expires, the refresh token can be used to obtain a new access token. The refresh token is returned as part of the JSON response when a verification code is used to obtain the access token:

{
        "access_token": "28d96a4e-9a31-479b-abc8-17ee1e8c9906",
        "token_type": "bearer",
        "refresh_token": "2583fd78-bd88-4c2b-afc0-fb231b37d95f",
        "expires_in": 43199,
        "scope": "read write"
}

The refresh token must be securely persisted and can be used to request a new access token when the previous access token expires:

$ curl 'https://api.sandbox.genesys-pgr.org/oauth/token?grant_type=refresh_token&client_id=CLIENTID&client_secret=SECRET&redirect_uri=oob&refresh_token=OAUTH-REFRESH-TOKEN'

2. Client errors

The API returns descriptive information in the response body about why the request failed to execute.

2.1. 401 Unauthorized

401 Unauthorized indicates that the request did not include valid authentication data. Check your OAuth access token.

401 Unauthorized error message

HTTP/1.1 401 Unauthorized
Content-Type: application/json;charset=UTF-8
...
WWW-Authenticate: Bearer realm="genesys2", error="unauthorized", error_description="An Authentication object was not found in the SecurityContext"

{"error":"unauthorized","error_description":"An Authentication object was not found in the SecurityContext"}

3. Managing passport data

Passport data is based on the FAO/Bioversity Multi-crop Passport Descriptors (MCPD V.2.1) format.

Accession records are upserted, meaning that:

when the matching accession record exists, it will be updated.
when it does not exist, a new record will be created.

Accession data in the database will be updated with whatever data is provided in the request JSON. When a piece of information is not provided in JSON, it will not be modified. If it is set to null it will be removed from the Genesys database.

3.1. Accession identity

Prior to full adoption of DOIs for germplasm, accessions could be identified by the holding institute code (instituteCode) and the accession number (accessionNumber). However, genebanks maintaining two or more crop collections sometimes use identical accession numbers in separate crop collections.

For this reason, Genesys uses the instituteCode, accessionNumber and GENUS triplet to uniquely identify an accession. For accessions with a digital object identifier (DOI) assigned in the ITPGRFA Secretariat Global Information System (GLIS), it will use the DOI to uniquely identify the record.

Identifiers in an accession JSON object


       
        
         
  
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          {
        "doi": "10.1054/12A1~", (1)
        "instituteCode": "NGA039", (2)
        "accessionNumber": "TMp-123", (3)
        "taxonomy": {
                "genus": "Musa", (4)
        },
        ...
}

1	DOI of the accession as registered in GLIS
2	Holding institute code (instituteCode)
3	Accession number (accessionNumber)
4	Genus (GENUS)

3.2. JSON data model

The JSON data model of accession passport data closely follows MCPD definitions, but uses human readable property names. Collecting data is grouped under coll key, taxonomic data under taxonomy and geographic data under geo key.

By default, institutes in Genesys are configured to "Use unique accession numbers within the institute". The accession JSON object must provide two identifying elements: instituteCode and accessionNumber.

In cases where accession numbers are not unique within the institute, taxonomy.genus is used to identify the unique accession within the institute. In such a case the Accession JSON object must always provide three identifying elements: instituteCode, accessionNumber and taxonomy.genus. All other fields are optional.

Example fields in an accession JSON object


       
        
         
  
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          {
        "doi": "10.1231/14S41Q",
        "instituteCode": "XYZ111",
        "accessionNumber": "M12345",
        "cropName": "banana",
        "taxonomy": {
                "genus": "Musa",
                "species": "acuminata",
                "spAuthor": "Colla",
                "subtaxa": "var. sumatrana",
                "subtAuthor": "(Becc.) Nasution"
        },
        "origCty": "NGA",
        "acquisitionDate": "20010301",
        "mlsStatus": true,
        "inTrust": false,
        "available": true,
        "historic": false,
        "storage": [ 10, 20 ],
        "sampStat": 200,
        "duplSite": [ "BEL084" ],
        "breederCode": [ "NGA039" ],
        "ancest": "PED/IG*REE",
        "remarks": [ "remark1", "remark2" ],
        "acceUrl": "https://my-genebank.org/accession/1",
        "geo": {
                ... (1)
        },
        "coll": {
                ... (2)
        }
}

1	JSON object with geographic data
2	JSON object with collecting data

3.3. Geographic data JSON model

The geo field in accession JSON captures geographic data.

Geographic data in a JSON object


       
        
         
  
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          {
        "latitude": 13.12312,
        "longitude": 42.2321,
        "elevation": 123.2,
        "uncertainty": 2000.0,
        "datum": "WGS84",
        "method": "GPS"
}

Table 2. Relevant MCPD descriptors
Field name	Description
DECLATITUDE	Latitude expressed in decimal degrees. Positive values are north of the Equator; negative values are south of the Equator (e.g. `-44.6975`).
DECLONGITUDE	Longitude expressed in decimal degrees. Positive values are east of the Greenwich Meridian; negative values are west of the Greenwich Meridian (e.g. `+120.9123`).
ELEVATION	Elevation of collecting site expressed in meters above sea level. Negative values are not allowed.
COORDUNCERT	Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.
COORDDATUM	The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and longitude are based (e.g. `WGS84`, `ETRS89`, `NAD83`). The GPS uses the WGS84 datum.
GEOREFMETH	The georeferencing method used (`GPS`, determined from `map`, `gazetteer`, or `estimated using software`). Leave the value empty if georeferencing method is not known.

3.4. Collecting data JSON model

The coll field in accession JSON captures collecting data.

Collecting data in a JSON object


       
        
         
  
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          {
        "collDate": "1990----",
        "collSite": "7km south of Curitiba in the state of Parana",
        "collNumb": "C90-23",
        "collSrc": 12,
        "collCode": [ "PER001" ],
        "collName": null,
        "collInstAddress": null,
        "collMissId": "C90"
}

Table 3. Relevant MCPD descriptors
Field name	Description
COLLDATE	Collecting date of the sample, in the format `YYYYMMDD`. Missing data (`MM` or `DD`) may be indicated with two hyphens or two zeros.
COLLSITE	Location information below the country level that describes where the accession was collected, preferably in English. This might include the distance in kilometers and direction from the nearest town, village or map grid reference point (e.g. `7km south of Curitiba in the state of Parana`).
COLLNUMB	Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. `FM9909`). This identifier is essential for identifying duplicates held in different collections.
COLLSRC	Collecting/acquisition source.
COLLCODE	FAO WIEWS code of the institute that collected the sample.
COLLNAME	Name of the institute that collected the sample. This descriptor should only be used if COLLCODE cannot be filled because the FAO WIEWS code for this institute is not available.
COLLINSTADDRESS	Address of the institute that collected the sample. This descriptor should only be used if COLLCODE cannot be filled because the FAO WIEWS code for this institute is not available.
COLLMISSID	Identifier of the collecting mission as used by the collecting institute (e.g. `CIATFOR-052`, `CN426`).

3.5. Clearing existing values

To reset or clear an existing value in the accession passport data, it should be provided as null. Not providing a field means the field in the database should not be modified.

Clearing the country of provenance from an accession record by sending a null value


       
        
         
  
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          {
        "instituteCode": "NGA039",
        "accessionNumber": "TMp-123",
        "taxonomy": {
                "genus": "Musa"
        },
        "origCty": null
}

3.6. Insert or update accessions

REST endpoint URL /api/v1/acn/{instituteCode}/upsert allows for inserting new accessions or updating existing records in Genesys. It accepts a JSON array of Accession JSON objects. The array provides for sending batches of 50 or 100 accessions in one call, reducing the HTTP overhead and improving performance.

Only the instituteCode and accessionNumber are required (and in some cases the taxonomy.genus). The server will return an error when the instituteCode of JSONs does not match the instituteCode in the URL!

3.7. Deleting accessions

With the introduction of permanent identifiers for accession records in Genesys we have also introduced the accession archive. The archive holds passport data for accession records that have been deleted from the active database.

REST endpoint URL /api/v1/acn/{instituteCode}/delete accepts an array of instituteCode, accessionNumber, genus triplets and deletes the corresponding accession records from Genesys. The DELETE permission is required for this operation.

The delete operation will fail if C&E data exists for any accessions listed.

Deleting three accessions from the active database


       
        
         
  
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          POST /api/v1/acn/SYR002/delete

[{
        "instituteCode": "SYR002",
        "accessionNumber": "12345",
        "taxonomy": { "genus": "Vicia" }
}, {
        "instituteCode": "SYR002",
        "accessionNumber": "12345",
        "taxonomy": { "genus": "Vicia" }
}, {
        "instituteCode": "SYR002",
        "accessionNumber": "IG 1",
        "taxonomy": { "genus": "Vicia" }
}]

3.8. Migrating from API v0

The v1 API uses a more self-explanatory JSON schema, adopting the internal Genesys property names in JSON de-/serialization, reducing the number of lines of code requried to parse and handle JSON input and output.

While the change made to the Java code are easier to read and maintain (for us), it requires data providers (you) to adopt the new naming scheme and update your software.

The primary change is the move from /api/*v0*/... endpoints to /api/*v1*/.... API v1 accepts and returns slightly different JSON compared to API v0.

Upgrade to v1 as soon as possible. The v0 API endpoints will be made obsolete in February 2020.

Genesys requires that breederCode, duplSite, collCode or donorCode use FAO WIEWS codes. Updating data will fail if existing or new records use invalid format (must be XXX000 or XXX0000).

3.8.1. Core accession properties

Table 4. Updated core properties
v0	v1	Notes
`instCode`	`instituteCode`	Holder institute code. Renamed for clarity.
`acceNumb`	`accessionNumber`	Accession number. Renamed for clarity.
`acqDate`	`acquisitionDate`	Date of acquisition. Renamed for clarity.
`bredCode`	`breederCode`	FAO WIEWS code of the institute that bred the material. Renamed for clarity. Accepts multiple values: `[ "XXX000", "YYY000" ]`
`bredName`	`breederName`	Name of the institute that bred the material. Renamed for clarity. Accepts multiple values: `[ "IITA", "CIMMYT" ]`
`mlsStat`	`mlsStatus`	MLS Status.
`orgCty`	`origCty`	ISO3166 code of provenance of material.

3.8.2. Taxonomic data

All taxonomic data was in the root JSON in v0 and is now grouped under taxonomy property.

Table 5. Updated properties for taxonomic data
v0	v1	Notes
`genus`	`taxonomy.genus`
`species`	`taxonomy.species`
`spauthor`	`taxonomy.spAuthor`	Note the uppercase `A`.
`subtaxa`	`taxonomy.subtaxa`
`subtauthor`	`taxonomy.subtAuthor`	Note the uppercase `A`.

3.8.3. Geographic data

Properties for geographic data under geo key are renamed:

Table 6. Updated properties for `geo` data
v0	v1	Notes
`geo.coordUncert`	`geo.uncertainty`	Distance of uncertainty of coordinates in meters.
`geo.coordDatum`	`geo.datum`	`WGS84` is most commonly used.
`geo.georefMeth`	`geo.method`	Method of georeferencing, text. Use values `GPS`, `Map` or similar.

3.8.4. Collecting data

Properties for collecting data in coll property are upgraded to support multiple values:

Table 7. Updated properties for `coll` data
v0	v1	Notes
`coll.collCode`	Same	Accepts multiple FAO WIEWS codes: `[ "XXX000", "ZZZ0000" ]`
`coll.collName`	Same	Accepts multiple values: `[ "collName1", "collName2" ]`
`coll.collInstAddress`	Same	Accepts multiple values: `[ "collInstAddress1", "collInstAddress2" ]`

4. Managing accession images

Institutes can upload accession images to the Genesys repository. Genesys will store and maintain images and metadata provided by institutes and display the images with accession passport data.

Genesys supports image galleries only for institutes that use unique ACCENUMB within their institute.

Managing accession images in Genesys is done through methods available in the /api/v0/img/{instCode}/ namespace.

4.1. Listing existing galleries

To list existing accession image galleries for the INSTCODE, you must have the WRITE or CREATE permission on the institute record. Issue a GET request to the /api/v0/img/{instCode}/_galleries endpoint:

$ curl 'https://api.sandbox.genesys-pgr.org/api/v0/img/XXX001/_galleries?page=1' -i -X GET \
    -H 'Content-Type: application/json'

4.1.1. Path parameters

Table 8. `/api/v0/img/{instCode}/_galleries`
Parameter	Description
`+instCode+`	Institute WIEWS code (e.g. NGA039)

4.1.2. Request parameters

Parameter Description

Parameter	Description
`+page+`	The page to return (1 is first page)

+page+

The page to return (1 is first page)

4.1.3. Server response

The object returned by Genesys contains pagination information and basic image gallery data in the content element.

JSON content element returned for an INSTCODE request


        
         
          
  
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           {
        "content": [{
                "uuid": "4422e87e-52fe-38ef-b04a-079e663dd3da",
                "version": 0,
                "instCode": "XXX001",
                "instEmail": "institute@localhost",
                "state": 0,
                "createdDate": null,
                "lastModifiedDate": null,
                "lastReminderDate": null
        }], (1)
        "last": true,
        "totalElements": 1, (2)
        "totalPages": 1, (3)
        "size": 10, (4)
        "number": 0,
        "sort": [{
                "direction": "DESC",
                "property": "createdDate",
                "ignoreCase": false,
                "nullHandling": "NATIVE",
                "ascending": false
        }],
        "first": true,
        "numberOfElements": 1 (5)
}

1	Array containing request information
2	Number of elements in the Genesys database
3	Number of pages
4	Page size
5	Number of elements in the `content` array

Path Type Description

Path	Type	Description
`+content+`	`+Array+`	Array containing request headers
`+content[0].uuid+`	`+String+`	Request UUID
`+content[0].instCode+`	`+String+`	WIEWS institute code
`+content[0].instEmail+`	`+String+`	Institute email address to which request was relayed
`+content[0].state+`	`+Number+`	Request state
`+content[0].createdDate+`	`+Number+`	Date when request was created
`+content[0].lastReminderDate+`	`+Null+`	Date when request was last relayed to specified email address
`+content[0].sourceRequest+`	`+String+`	The UUID of source request
`+numberOfElements+`	`+Number+`	Number of records in the content array
`+totalElements+`	`+Number+`	Total number of requests in Genesys belonging to this institute
`+size+`	`+Number+`	Page size
`+number+`	`+Number+`	Current page number
`+totalPages+`	`+Number+`	Page count
`+sort+`	`+Array+`	Array sorting details

+content+

+Array+

Array containing request headers

+content[0].uuid+

+String+

Request UUID

+content[0].instCode+

+String+

WIEWS institute code

+content[0].instEmail+

+String+

Institute email address to which request was relayed

+content[0].state+

+Number+

Request state

+content[0].createdDate+

+Number+

Date when request was created

+content[0].lastReminderDate+

+Null+

Date when request was last relayed to specified email address

+content[0].sourceRequest+

+String+

The UUID of source request

+numberOfElements+

+Number+

Number of records in the content array

+totalElements+

+Number+

Total number of requests in Genesys belonging to this institute

+size+

+Number+

Page size

+number+

+Number+

Current page number

+totalPages+

+Number+

Page count

+sort+

+Array+

Array sorting details

4.2. Accepted image formats

Genesys allows for images in JPG and PNG format.

4.3. Adding images to accessions

To add images to an accession you must first upload the image to Genesys with a PUT request, with the image bytes in the request body:

$ curl 'https://api.sandbox.genesys-pgr.org/api/v0/img/XXX001/acn/ACC001/?originalFilename=IMG0012.jpg' -i -X PUT -H 'Content-Type: image/jpeg' -d @path/to/IMG0012.jpg

The request Content-Type header must be set to the image content type (e.g. image/png or image/jpeg).

4.3.1. Path parameters

Table 9. `/api/v0/img/{instCode}/acn/{acceNumb}/`
Parameter	Description
`+instCode+`	Institute WIEWS code (e.g. NGA039)
`+acceNumb+`	Existing ACCENUMB in the institute

4.3.2. Request parameters

Parameter Description

Parameter	Description
`+originalFilename+`	Filename of the image (e.g. IMG00121.jpg)

+originalFilename+

Filename of the image (e.g. IMG00121.jpg)

4.3.3. Server response

As Genesys accepts the image data, it will create a blank image metadata record and return the detailed image data, including the image UUID which is required for subsequent updates of the image metadata or the image bytes.

Server response to added image data


        
         
          
  
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           {
        "id": 1,
        "contentType": "image/jpeg",
        "format": "image/jpeg",
        "uuid": "16648001-72b5-4295-ad29-169a414ee8f1",
        "identifier": "urn:uuid:16648001-72b5-4295-ad29-569a414ee8f1",
        "originalFilename": "maize.jpg",
        "extension": ".jpg",
        "path": "/accessions/XXX001/acn/ACC001/",
        "filename": "16648001-72b5-4295-ad29-569a414ee8f1.jpg",
        "url": "/accessions/XXX001/acn/ACC001/16648001-72b5-4295-ad29-569a414ee8f1.jpg",
        "sha1Sum": "160599e1ccd66e132a9b92bc845a9591fe948586",
        "md5Sum": "c1887df421746e30a41b898956ea1f3e",
        "width": 640,
        "height": 427,
        "orientation": "LANDSCAPE",
        "title": null,
        "subject": null,
        "description": null,
        "creator": null,
        "created": null,
        "rightsHolder": null,
        "accessRights": null,
        "license": null,
        "extent": null,
        "bibliographicCitation": null,
        "createdDate": null,
        "lastModifiedDate": null,
        "originalUrl": null,
        "dateRetrieved": null,
        "dateSubmitted": null,
        "modified": null,
}

You will observe that most metadata is null, but the image bytes are now stored in the Genesys repository. Genesys also determines the image width, height and orientation from the image.

Path Type Description

Path	Type	Description
`+uuid+`	`+String+`	UUID of the image in the Genesys repository
`+identifier+`	`+String+`	Unique identifier assigned to the image by Genesys
`+originalFilename+`	`+String+`	The original filename that you have provided
`+extension+`	`+String+`	Image extension derived from original filename (e.g. .jpg)
`+contentType+`	`+String+`	The content type of the image (autodetected when possible)
`+format+`	`+String+`	Image format
`+size+`	`+Number+`	Image size in bytes
`+folder+`	`+String+`	Location (directory) of the image in the Genesys repository
`+filename+`	`+String+`	The generated filename
`+storageFolder+`	`+String+`	The folder where bytes are stored
`+storagePath+`	`+String+`	Path to the bytes in storage
`+metadataFilename+`	`+String+`	The generated filename for image metadata
`+sha1Sum+`	`+String+`	SHA1 hash of the image bytes
`+md5Sum+`	`+String+`	MD5 hash of the image bytes
`+width+`	`+Number+`	Image width in pixels (autodetected)
`+height+`	`+Number+`	Image height in pixels (autodetected)
`+orientation+`	`+String+`	LANDSCAPE or PORTRAIT orientation of the image (autodetected)
`+thumbnailPath+`	`+String+`	Thumbnails folder

+uuid+

+String+

UUID of the image in the Genesys repository

+identifier+

+String+

Unique identifier assigned to the image by Genesys

+originalFilename+

+String+

The original filename that you have provided

+extension+

+String+

Image extension derived from original filename (e.g. .jpg)

+contentType+

+String+

The content type of the image (autodetected when possible)

+format+

+String+

Image format

+size+

+Number+

Image size in bytes

+folder+

+String+

Location (directory) of the image in the Genesys repository

+filename+

+String+

The generated filename

+storageFolder+

+String+

The folder where bytes are stored

+storagePath+

+String+

Path to the bytes in storage

+metadataFilename+

+String+

The generated filename for image metadata

+sha1Sum+

+String+

SHA1 hash of the image bytes

+md5Sum+

+String+

MD5 hash of the image bytes

+width+

+Number+

Image width in pixels (autodetected)

+height+

+Number+

Image height in pixels (autodetected)

+orientation+

+String+

LANDSCAPE or PORTRAIT orientation of the image (autodetected)

+thumbnailPath+

+String+

Thumbnails folder

4.4. Updating image metadata

After a successful upload of an image to the Genesys repository, you are able to manage the image metadata.

Example image metadata


       
        
         
  
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          {
        "title": "Leaf of ACC001",
        "subject": "ACC001",
        "description": "Image of leaf of ACC001 taken ...",
        "creator": "John Doe",
        "rightsHolder": "International Institute of Accessions (IIA)",
        "accessRights": "Access rights",
        "license": "https://creativecommons.org/publicdomain/zero/1.0/",
        "bibliographicCitation": "Genesys Museum in Bonn. Digital image. Accession Imagery. Genesys. Web. 9 August 2016."
}

Path Type Description

Path	Type	Description
`+title+`	`+String+`	Title is a property that refers to the name or names by which a resource is formally known
`+subject+`	`+String+`	The Subject described or pictured in the resource, accession number
`+description+`	`+String+`	Description of the content of a resource. The description is a potentially rich source of indexable terms and assist the users in their selection of an appropriate resource.
`+creator+`	`+String+`	An entity primarily responsible for making the resource
`+created+`	`+String+`	A point or period of time when the resource was created by the Creator
`+rightsHolder+`	`+String+`	Person or an organization owning or managing rights over this resource
`+accessRights+`	`+String+`	Access rights provides information about restrictions to view, search or use a resource based on attributes of the resource itself or the category of user.
`+license+`	`+String+`	Legal document giving official permission to do something with the resource. E.g. http://www.gnu.org/licenses/gpl.html
`+extent+`	`+String+`	Size (e.g. bytes, pages, inches, etc.) or duration (e.g. hours, minutes, days, etc.) of a resource
`+bibliographicCitation+`	`+String+`	Formal bibliographic citation for the resource

+title+

+String+

Title is a property that refers to the name or names by which a resource is formally known

+subject+

+String+

The Subject described or pictured in the resource, accession number

+description+

+String+

Description of the content of a resource. The description is a potentially rich source of indexable terms and assist the users in their selection of an appropriate resource.

+creator+

+String+

An entity primarily responsible for making the resource

+created+

+String+

A point or period of time when the resource was created by the Creator

+rightsHolder+

+String+

Person or an organization owning or managing rights over this resource

+accessRights+

+String+

Access rights provides information about restrictions to view, search or use a resource based on attributes of the resource itself or the category of user.

+license+

+String+

Legal document giving official permission to do something with the resource. E.g. http://www.gnu.org/licenses/gpl.html

+extent+

+String+

Size (e.g. bytes, pages, inches, etc.) or duration (e.g. hours, minutes, days, etc.) of a resource

+bibliographicCitation+

+String+

Formal bibliographic citation for the resource

An example curl request is:

$ curl 'https://api.sandbox.genesys-pgr.org/api/v0/img/XXX001/acn/ACC001/8ecdea45-9101-40f8-9877-a17c44a90438/_metadata' -i -X PUT \
    -H 'Content-Type: application/json' \
    -d '{"active":true,"title":"Leaf of ACC001","subject":"ACC001","description":"Image of leaf of ACC001 taken ...","creator":"John Doe","created":"August 2016","rightsHolder":"International Institute of Accessions (IIA)","accessRights":"Access rights","license":"https://creativecommons.org/publicdomain/zero/1.0/","extent":"4000x2000 pixels, 10MB","bibliographicCitation":"Genesys Museum in Bonn. Digital image. Accession Imagery. Genesys. Web. 9 August 2016.","size":0,"width":0,"height":0,"_class":"RepositoryImage"}'

4.4.1. Path parameters

Table 10. `/api/v0/img/{instCode}/acn/{acceNumb}/{uuid}/_metadata`
Parameter	Description
`+instCode+`	Institute WIEWS code (e.g. NGA039)
`+acceNumb+`	Existing ACCENUMB in the institute
`+uuid+`	UUID of the image in the gallery of this accession

4.4.2. Response fields

Server response with updated image metadata


        
         
          
  
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           {
        "id": 1,
        "uuid": "1e23549e-a882-40b4-abc8-0a4708ba7ff3",
        "path": "/accessions/XXX001/acn/ACC001/",
        "originalFilename": "maize.jpg",
        "extension": ".jpg",
        "title": "Leaf of ACC001",
        "subject": "ACC001",
        "description": "Image of leaf of ACC001 taken ...",
        "creator": "John Doe",
        "created": null,
        "rightsHolder": "International Institute of Accessions (IIA)",
        "accessRights": "Access rights",
        "license": "https://creativecommons.org/publicdomain/zero/1.0/",
        "contentType": "image/jpeg",
        "extent": null,
        "bibliographicCitation": "Genesys Museum in Bonn. Digital image. Accession Imagery. Genesys. Web. 9 August 2016.",
        "createdDate": null,
        "lastModifiedDate": null,
        "originalUrl": null,
        "dateRetrieved": null,
        "sha1Sum": "160599e1ccd66e132a9b92bc845a9591fe948586",
        "md5Sum": "c1887df421746e30a41b898956ea1f3e",
        "width": 640,
        "height": 427,
        "orientation": "LANDSCAPE",
        "identifier": "urn:uuid:1e23549e-a882-40b4-abc8-0a4708ba7ff3",
        "dateSubmitted": null,
        "modified": null,
        "format": "image/jpeg",
        "url": "/accessions/XXX001/acn/ACC001/1e23549e-a882-40b4-abc8-0a4708ba7ff3.jpg",
        "filename": "1e23549e-a882-40b4-abc8-0a4708ba7ff3.jpg"
}

Path Type Description

Path	Type	Description
`+originalFilename+`	`+String+`	The original filename that you have provided
`+folder+`	`+String+`	Location (directory) of the image in the Genesys repository
`+filename+`	`+String+`	The generated filename
`+storageFolder+`	`+String+`	The folder where bytes are stored
`+width+`	`+Number+`	Image width in pixels (autodetected)
`+height+`	`+Number+`	Image height in pixels (autodetected)
`+orientation+`	`+String+`	LANDSCAPE or PORTRAIT orientation of the image (autodetected)
`+format+`	`+Null+`	Image format
`+identifier+`	`+String+`	Permanent unique identifier of the resource. Commonly a Uniform Resource Locator (URL).
`+title+`	`+String+`	Title is a property that refers to the name or names by which a resource is formally known
`+subject+`	`+String+`	The Subject described or pictured in the resource, accession number
`+description+`	`+String+`	Description of the content of a resource. The description is a potentially rich source of indexable terms and assist the users in their selection of an appropriate resource.
`+creator+`	`+String+`	An entity primarily responsible for making the resource
`+created+`	`+String+`	A point or period of time when the resource was created by the Creator
`+rightsHolder+`	`+String+`	Person or an organization owning or managing rights over this resource
`+accessRights+`	`+String+`	Access rights provides information about restrictions to view, search or use a resource based on attributes of the resource itself or the category of user.
`+license+`	`+String+`	Legal document giving official permission to do something with the resource. E.g. http://www.gnu.org/licenses/gpl.html
`+extent+`	`+String+`	Size (e.g. bytes, pages, inches, etc.) or duration (e.g. hours, minutes, days, etc.) of a resource
`+bibliographicCitation+`	`+String+`	Formal bibliographic citation for the resource
`+size+`	`+Number+`	Image size in bytes
`+width+`	`+Number+`	Image width in pixels
`+height+`	`+Number+`	Image height in pixels

+originalFilename+

+String+

The original filename that you have provided

+folder+

+String+

Location (directory) of the image in the Genesys repository

+filename+

+String+

The generated filename

+storageFolder+

+String+

The folder where bytes are stored

+width+

+Number+

Image width in pixels (autodetected)

+height+

+Number+

Image height in pixels (autodetected)

+orientation+

+String+

LANDSCAPE or PORTRAIT orientation of the image (autodetected)

+format+

+Null+

Image format

+identifier+

+String+

Permanent unique identifier of the resource. Commonly a Uniform Resource Locator (URL).

+title+

+String+

Title is a property that refers to the name or names by which a resource is formally known

+subject+

+String+

The Subject described or pictured in the resource, accession number

+description+

+String+

Description of the content of a resource. The description is a potentially rich source of indexable terms and assist the users in their selection of an appropriate resource.

+creator+

+String+

An entity primarily responsible for making the resource

+created+

+String+

A point or period of time when the resource was created by the Creator

+rightsHolder+

+String+

Person or an organization owning or managing rights over this resource

+accessRights+

+String+

Access rights provides information about restrictions to view, search or use a resource based on attributes of the resource itself or the category of user.

+license+

+String+

Legal document giving official permission to do something with the resource. E.g. http://www.gnu.org/licenses/gpl.html

+extent+

+String+

Size (e.g. bytes, pages, inches, etc.) or duration (e.g. hours, minutes, days, etc.) of a resource

+bibliographicCitation+

+String+

Formal bibliographic citation for the resource

+size+

+Number+

Image size in bytes

+width+

+Number+

Image width in pixels

+height+

+Number+

Image height in pixels

5. Managing requests

Institutes can allow users to request material through Genesys. Genesys will validate the user’s email address (by waiting for them to click the confirmation link sent to their address) and also check if the user is registered with ITPGRFA’s Easy-SMTA database.

Genesys maintains a database of requests received, confirmed and dispatched to genebanks holding the requested materials. This API allows genebanks to retrieve the request data from Genesys for automated integration into their existing information systems.

A client may request material from several different genebanks in one session. Genesys splits the request and dispatches sub-requests to email addresses registered with individual genebanks.

Managing crop data in Genesys is done through methods available in the /api/v0/requests namespace.

5.1. Listing requests

To list all requests for a given INSTCODE, you must have the ADMINISTRATOR permission on the institute record. Issue a GET request to the /api/v0/requests/{instCode} endpoint:

$ curl 'https://api.sandbox.genesys-pgr.org/api/v0/requests/XXX001?page=0' -i -X GET

5.1.1. Path parameters

Table 11. `/api/v0/requests/{instCode}`
Parameter	Description
`+instCode+`	Institute WIEWS code (e.g. NGA039)

5.1.2. Request parameters

Parameter Description

Parameter	Description
`+page+`	Page to request from the server

+page+

Page to request from the server

5.1.3. Server response

The object returned by Genesys contains pagination information and basic request data in the content element.

Request data returned by the server


        
         
          
  
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           {
        "content": [{
                "uuid": "4422e87e-52fe-38ef-b04a-079e663dd3da",
                "version": 0,
                "instCode": "XXX001",
                "instEmail": "institute@localhost",
                "state": 0,
                "createdDate": null,
                "lastModifiedDate": null,
                "lastReminderDate": null
        }], (1)
        "last": true,
        "totalElements": 1, (2)
        "totalPages": 1, (3)
        "size": 10, (4)
        "number": 0,
        "sort": [{
                "direction": "DESC",
                "property": "createdDate",
                "ignoreCase": false,
                "nullHandling": "NATIVE",
                "ascending": false
        }],
        "first": true,
        "numberOfElements": 1, (5)
}

1	Array containing request information
2	Number of elements in the Genesys database
3	Number of pages
4	Page size
5	Number of elements in the `content` array

Path Type Description

Path	Type	Description
`+content+`	`+Array+`	Array containing request headers
`+content[0].uuid+`	`+String+`	Request UUID
`+content[0].instCode+`	`+String+`	WIEWS institute code
`+content[0].instEmail+`	`+String+`	Institute email address to which request was relayed
`+content[0].state+`	`+Number+`	Request state
`+content[0].createdDate+`	`+Number+`	Date when request was created
`+content[0].lastReminderDate+`	`+Null+`	Date when request was last relayed to specified email address
`+content[0].sourceRequest+`	`+String+`	The UUID of source request
`+numberOfElements+`	`+Number+`	Number of records in the content array
`+totalElements+`	`+Number+`	Total number of requests in Genesys belonging to this institute
`+size+`	`+Number+`	Page size
`+number+`	`+Number+`	Current page number
`+totalPages+`	`+Number+`	Page count
`+sort+`	`+Array+`	Array sorting details

+content+

+Array+

Array containing request headers

+content[0].uuid+

+String+

Request UUID

+content[0].instCode+

+String+

WIEWS institute code

+content[0].instEmail+

+String+

Institute email address to which request was relayed

+content[0].state+

+Number+

Request state

+content[0].createdDate+

+Number+

Date when request was created

+content[0].lastReminderDate+

+Null+

Date when request was last relayed to specified email address

+content[0].sourceRequest+

+String+

The UUID of source request

+numberOfElements+

+Number+

Number of records in the content array

+totalElements+

+Number+

Total number of requests in Genesys belonging to this institute

+size+

+Number+

Page size

+number+

+Number+

Current page number

+totalPages+

+Number+

Page count

+sort+

+Array+

Array sorting details

5.2. Request details

To retrieve request details from Genesys:

$ curl 'https://api.sandbox.genesys-pgr.org/api/v0/requests/XXX001/r/14784c7a-e548-4f04-a258-94fd534db617' -i -X GET \
    -H 'Content-Type: application/json'

5.2.1. Path parameters

Table 12. `/api/v0/requests//{instCode}/r/{uuid}`
Parameter	Description
`+instCode+`	Institute WIEWS code (e.g. NGA039)
`+uuid+`	UUID of the request

5.2.2. Server response


        
         
          
  
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           {
        "uuid": "7ecb3c6e-63d8-3869-b2c7-28571c9e2864",
        "version": 0,
        "instCode": "XXX001",
        "instEmail": "institute@localhost",
        "state": 0,
        "createdDate": null,
        "lastModifiedDate": null,
        "lastReminderDate": null
}

Path Type Description

Path	Type	Description
`+uuid+`	`+String+`	The request UUID
`+version+`	`+Number+`	Record version indicator
`+instCode+`	`+String+`	WIEWS code of the institute handling the request
`+instEmail+`	`+String+`	Email address to which Genesys sends notifications
`+sourceRequest+`	`+String+`	The UUID of source request
`+state+`	`+Number+`	The request STATE indicator
`+lastReminderDate+`	`+Null+`	Date of last email notification sent to institute

+uuid+

+String+

The request UUID

+version+

+Number+

Record version indicator

+instCode+

+String+

WIEWS code of the institute handling the request

+instEmail+

+String+

Email address to which Genesys sends notifications

+sourceRequest+

+String+

The UUID of source request

+state+

+Number+

The request STATE indicator

+lastReminderDate+

+Null+

Date of last email notification sent to institute

6. Managing crop data

Genesys maintains a database of crops and crop groups (e.g. forages). In addition to the general description, each crop defines a list of taxonomic rules that determine which taxonomies are included (or excluded) in the group.

Crops and crop groups are referred to and identified by the crop’s short name. The short name placeholder in documentation below is marked by {shortName}. The short name should have no spaces and it should contain US-ASCII characters only (a-Z, 0-9).

6.1. Crop taxonomic rules

The common crop name of an accession in Genesys is determined by its taxonomy. For example, the crop banana includes accessions of the genus Musa.

Each crop and crop group defines its own taxonomic rules.
The genus, species and sub-species data of an accession is matched against all taxonomic rules.
1. The accession is linked with all matching crops.
2. The accession may have more than one "crop".

Managing crop data in Genesys is done through methods available in the /api/v0/crops namespace.

6.2. Listing all crops

A number of crops and crop groups are usually defined and used in Genesys. To list all crops, issue a GET request to the /api/v0/crops/ endpoint:

$ curl 'https://api.genesys-pgr.org/api/v2/crops' -i -X GET \
    -H 'Content-Type: application/json'

The result is a JSON array of all crops in Genesys.

Start of a JSON array listing all crops in Genesys


       
        
         
  
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          [{
        "id": 27,
        "version": 1,
        "rdfUri": null,
        "shortName": "apple",
        "name": "Apple",
        "description": null,
        "i18n": "{\"name\":{\"fa\":\"سیب\"}}"
}, {
        "id": 1,
        "shortName": "banana",
        "name": "Banana", ... (1)
}, {
        "shortName": "barley",
        "name": "Barley", ...
},
...]

1	Some JSON elements removed for readability.

6.3. Retrieving crop data

The crop details are retrievable with a GET request to /api/v0/crops/{shortName}.

Table 13. `/api/v2/crops/{shortName}`
Parameter	Description
`+shortName+`	Crop short name or code (e.g. maize)

Sample curl request to fetch maize crop definition

$ curl 'https://api.genesys-pgr.org/api/v2/crops/maize' -i -X GET \
    -H 'Content-Type: application/json'

The JSON representation of a single crop record includes the following fields.

Table 14. Fields of crop records
Path	Type	Description
`+id+`	`+Number+`	Autogenerated ID
`+version+`	`+Number+`	Record version
`+name+`	`+String+`	Crop name in English
`+shortName+`	`+String+`	Crop short name or code (e.g. maize)
`+description+`	`+String+`	Crop description in English
`+rdfUri+`	`+String+`	URI of RDF term describing the crop
`+i18n+`	`+String+`	i18n map
`+otherNames+`	`+Array+`	Alternative spellings of the crop name

6.3.1. Taxonomic rules

The /api/v0/crops/{shortName}/rules endpoint exposes access to a crop’s taxonomic rules. We mentioned earlier that accessions with the genus Musa belong to bananas; similarly, accessions of the Zea genus belong to maize:

Maize taxonomic rules

Unresolved directive in api/crop.adoc - include::/builds/genesys-pgr/genesys-server/target/generated-snippets/crop-rules-list/curl-request.adoc[]

Result of request for maize taxonomic rules


        
         
          
  
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           [{
        "id": 24,
        "included": true, (1)
        "genus": "Zea", (2)
        "species": null, (3)
        "subtaxa": null, (4)
}]

1	The combination of genus, species and subtaxa can be either included or explicitly excluded from the crop.
2	An accession is included in maize when accession’s genus value is `Zea`.
3	Species field is `null` meaning that accession species is ignored by this rule.
4	Subtaxa field is `null` meaning that accession subtaxa value is ignored by this rule.

6.3.2. Exclusion rule

A rule can explicitly exclude accessions matching a particular combination of genus + species + subtaxa. This is useful, for example, in order to include all accessions of the Solanum genus except for selected species (e.g. Solanum melongena).

6.4. Registering a new crop

To create a new crop, a JSON with the following data must be submitted.

Data to register a crop


       
        
         
  
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          {
        "shortName": "maize",
        "name": "Maize",
        "description": "Crop description in EN"
}

Table 15. Minimum required data to register a crop
Path	Type	Description
`+shortName+`	`+String+`	Crop short name or code (e.g. maize)
`+name+`	`+String+`	Crop name in English
`+description+`	`+String+`	Crop description in English

The response is a single crop record as stored on the server.

Example request to register a new crop

$ curl 'https://api.genesys-pgr.org/api/v1/crops/save' -i -X POST \
    -H 'Content-Type: application/json' \
    -d '{"shortName":"rice","name":"Rice","description":"Crop description in EN"}'

6.5. Localization of crop title and description

The i18n field of the JSON crop object is a string encoded JSON object of a two level JSON formatted dictionary string with first level keys name (for the name field) and description (for the description field) and second level keys corresponding to ISO_639_2 encoded vernacular language tags.

Localized names and descriptions for genus Musa


       
        
         
  
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          {
        "name": {
                "en": "Musa",
                "es": "Musa",
                "ru": "Муса",
                "zh": "穆萨"
        },
        "description": {
                "en": "Bananas and plantains",
                "es": "Los bananos y plátanos",
                "ru": "Бананы и бананы",
                "zh": "香蕉和大蕉"
        }
}

6.6. Updating taxonomic rules

Taxonomic rules can be replaced using one call by providing the new list of rules as the body of the HTTP PUT call to /api/v0/crops/{shortName}/rules. To specify that all Triticum and Aegilops species should be included in wheat, you would send the following array of rules to /api/v0/crops/wheat/rules

Rule array to include multiple species in a crop


       
        
         
  
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          [{
        "included": true,
        "genus": "Triticum"
}, {
        "included": true,
        "genus": "Aegilops"
}]

Setting new taxonomic rules for the selected crop

Unresolved directive in api/crop.adoc - include::/builds/genesys-pgr/genesys-server/target/generated-snippets/crop-rules-update/curl-request.adoc[]

Taxonomic rule fields

Unresolved directive in api/crop.adoc - include::/builds/genesys-pgr/genesys-server/target/generated-snippets/crop-rules-update/request-fields.adoc[]

6.7. Deleting a crop

A crop record can be deleted by issuing an HTTP DELETE request to /api/v0/crops/{shortName}. This will remove the crop and crop rules from the system.

Deleting a crop

$ curl 'https://api.genesys-pgr.org/api/v1/crops/rice' -i -X DELETE \
    -H 'Content-Type: application/json'

7. Acknowledgements

Special thanks go to Luca Matteis and Richard Bruskiewich from Bioversity International who have contributed to the original documentation of the APIs.

فهرس المحتويات

1. Security
- 1.1. Obtaining the access token
- 1.2. Using the refresh token
2. Client errors
- 2.1. 401 Unauthorized
3. Managing passport data
4. Managing accession images
5. Managing requests
- 5.1. Listing requests
- 5.2. Request details
  - 5.2.1. Path parameters
  - 5.2.2. Server response
6. Managing crop data
7. Acknowledgements