General

Requests

/centre/zip

Returns a list of ZIP files in summary view


/centre/zip/issues

Returns a list of ZIP files with failures/warnings in summary view for greater than or equal to given created date of the file (Pagination is not effective for this endpoint as required data is controlled by creation date of the instance)


/centre/xml

Returns a list of XML files in summary view


/centre/xml/issues

Returns a list of XMLs with failures/warnings in summary view for greater than or equal to given created date of the file (Pagination is not effective for this endpoint as required data is controlled by creation date of the instance)


/xml/:idOrFilename

Returns all instances of an XMl file with the given filename or one result with the given id - :idOrFilename - The id or filename of the XML file


/zip/:zipIdOrFilename

Returns all XML files within the given ZIP file in summary view - :zipIdOrFilename - The id or filename of a ZIP file


/issues/zip/:zipIdOrFilename

Returns all XML files with failures and warnings within the given ZIP file in summary view - :zipIdOrFilename - The id or filename of a ZIP file


/zip/:zipIdOrFilename/:xmlIdOrFilename

Returns the contents of an XML file with the given id or filename - :zipIdOrFilename - The id or filename of a ZIP file - :xmlIdOrFilename - The id or filename of an XML file contained in the ZIP file


/specimen/:centre/:specimenId

Returns all instances of a specimen from the given centre for the given specimen - :centre - Phenotyping centre ILAR code. - :specimenId - The specimen for which to retrieve data for


/specimen/:centre

Returns all instances of a specimen from the given centre (Pagination is not effective for this endpoint as required data is controlled by crawling date for file) - :centre - Phenotyping centre ILAR code.


/specimen/experimentprocedure/:centre/:specimenId

Returns all experiment procedures for a specimen from a specific centre - :centre - Phenotyping centre ILAR code - :specimenId - The specimen for which to retrieve experiment procedure data for


/experimentprocedure/:centre

Returns all experiment procedures for the given centre (Pagination is not effective for this endpoint as required data is controlled by crawling date for xml file) - :centre - Phenotyping centre ILAR code.


/lineprocedure/:colonyId

Returns all submitted line procedures for a colony id - :colonyId - The colony id for which to retrieve line procedures for


/lineproc/:centre

Returns all line procedures for the given centre (Pagination is not effective for this endpoint as required data is controlled by crawling date for xml file) - :centre - Phenotyping centre ILAR code.


/linesummary/:centre/:colonyId

Returns all specimens, experiment procedures per specimen and all line procedures for a given colony for a specific centre.
- :centre - Phenotyping centre ILAR code - :colonyId - The colony for which to retrieve data for


/xml/meta/status

Returns a lookup of the xml statuses:

Id Status
1 pending
2 running
3 done
4 cancelled
5 failed

/pcv/meta/status

Returns a lookup of the xml statuses:

Id Status
0 failed
1 valid
2 active
4 pending
8 duplicate
16 status_coded
32 failed_overviews

/xml/meta/phase

Returns a lookup of the xml phases:

IdPhase
1 download
2 zip_name
3 zip_md5
4 unzip
5 xml_name
6 xsd
7 upload
8 data
9 context
10 overview
11 qc

Data structures

Datatype : logs[]

"logs": [
            {
                "line": 3,
                "column": 27,
                "message": "cvc-complex-type.2.4.b: The content of element 'centre' is not complete. One of '{\"http://www.mousephenotype.org/dcc/exportlibrary/datastructure/core/specimen\":mouse, \"http://www.mousephenotype.org/dcc/exportlibrary/datastructure/core/specimen\":embryo}' is expected.",
                "fatality": "Error"
            }
        ]

Datatype : experimentProcedures[]

"experimentProcedures": [
            {
                "id": 11819530,
                "xmlId": 631707,
                "experimentName": "HIS_CR1343-80_2019-02-22",
                "procedure": "IMPC_HIS_001",
                "specimen": "CR1343-80",
                "phenotypingCentre": "UCD",
                "sequenceId": null,
                "statusId": 1,
                "status": "valid",
                "ageInWeeks": 91.57,
                "created": 1558120560,
                "createdDate": "2019-05-17T20:16",
                "logs": [
                    {
                        "message": "'multi-focal' is not a valid name for ontologyTerm PATO:0001791 for OntologyParameter IMPC_HIS_131_001",
                        "parameterType": "OntologyParameter",
                        "parameterKey": "IMPC_HIS_131_001",
                        "fatality": "Warning"
                    },
                    {
                        "message": "'mild' is not a valid name for ontologyTerm PATO:0000394 for OntologyParameter IMPC_HIS_131_001",
                        "parameterType": "OntologyParameter",
                        "parameterKey": "IMPC_HIS_131_001",
                        "fatality": "Warning"
                    },
                    {
                        "message": "'degenerative change' is not a valid name for ontologyTerm MPATH:14 for OntologyParameter IMPC_HIS_129_001",
                        "parameterType": "OntologyParameter",
                        "parameterKey": "IMPC_HIS_129_001",
                        "fatality": "Warning"
                    }
                ],
                "dateOfExperiment": "2019-02-22T00:00"
            }
]

Datatype : specimens[]

"specimens": [
            {
                "id": 2432393,
                "specimen": "CR10246-201",
                "isBaseline": true,
                "zygosity": "WILD_TYPE",
                "sex": "FEMALE",
                "type": "mouse",
                "phenotypingCentre": "UCD",
                "pipeline": "UCD_001",
                "colony": null,
                "dateOfBirth": "2019-02-23T00:00",
                "xmlId": 631692,
                "statusId": 2,
                "status": "active",
                "created": 1558120138000,
                "createdDate": "2019-05-17T20:08:58",
                "strain": "C57BL/6NCrl",
                "project": "DTCC",
                "logs": []
            }
]

Datatype : lineProcedures[]

"lineProcedures": [
            {
                "id": 119379,
                "xmlId": 630532,
                "procedure": "IMPC_EVL_001",
                "colony": "CUBMB",
                "phenotypingCentre": "BCM",
                "sequenceId": null,
                "statusId": 8,
                "status": "duplicate",
                "created": 1557964919,
                "createdDate": "2019-05-16T01:01:59",
                "logs": []
            }
]

Datatype : validationLogs[]

"validationLogs": [
                    {
                        "message": "'Message for failure",
                        "parameterType": "Parameter Type", 
                        "parameterKey": "Parameter Key",
                        "fatality": "Warning/Error"
                    },
]