Tracker API Documentation

General


  • All requests are GET requests unless otherwise stated.
  • All requests, except /linesummary/:centre/:colonyId, can be paginated using the query parameters start and resultsize
    • start – offset
    • resultsize – max number of results to retrieve
    • Both parameters need to be > 0 or are otherwise ignored
    • By default pagination is disabled except if a resultsize > 0 is defined
      • The only exception is the /centre/xml request that has a default pagination of 100

Requests


/centre/zip?centre=:shortName

Returns a list of ZIP files in summary view

  • Takes additional parameters as query string:
    • centre – The centre short name, e.g Tcp
    • updatedSinceDate – The day when file has been crawled. The endpoint point will fetch all files with a date >= updatedSinceDate. The default value is null. If this value is passed unless resultsize is selected all the values would be returned. If its null default pagination would be 100
  • Example: https://api.mousephenotype.org/tracker/centre/zip?centre=Kmpc&start=0&resultsize=50

/centre/zip/issues?centre=:shortName

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

  • Takes additional parameters as query string:
    • centre – The centre short name, e.g Tcp
    • updatedSinceDate – The day when file has been crawled. The endpoint point will fetch all files with a date >= updatedSinceDate. The default value is one month before current date .
    • ignoreWarnings – If set as true it will exclude zip files that only contain xml files with validation warnings.
    • validationIssues – If set as true will return the zip files that contain xml files with validation issues.
    • xmlErrors – If set as true will return the zip files that contain xml files with xml errors.
    • zipErrors – If set as true will return the zip files having zip errors.
  • Filtering will be performed if any of the validationIssuesxmlErrorsignoreWarnings or zipErrors flags is set as true. If none of them is passed as an argument it will return everything. false values will not effect the result.
  • Example: https://api.mousephenotype.org/tracker/centre/zip/issues?centre=Kmpc&updatedSinceDate=2019-10-01&ignoreWarnings=true

/centre/xml?centre=:shortName

Returns a list of XML files in summary view


/centre/xml/issues?centre=:shortName

Returns a list of XMLs with failures/warnings in summary view for greater than or equal to given updatedSinceDate of the file which is the date when file has been crawled (Pagination is not effective for this endpoint as required data is controlled by date)

  • Takes additional parameters as query string:
    • centre – The centre short name, e.g Tcp
    • updatedSinceDate – The day when file has been crawled. The endpoint point will fetch all files with a date >= updatedSinceDate. The default value is one month before current date .
    • ignoreWarnings – If set as true it will exclude zip files that only contain xml files with validation warnings.
    • validationIssues – If set as true will return the zip files that contain xml files with validation issues.
    • xmlErrors – If set as true will return the zip files that contain xml files with xml errors.
  • Filtering will be performed if any of the validationIssuesxmlErrors or ignoreWarnings flags is set as true. If none of them is passed as an argument it will return everything. false values will not effect the result.
  • Example: https://api.mousephenotype.org/tracker/centre/xml/issues?centre=Kmpc&updatedSinceDate=2019-10-01&ignoreWarnings=true

/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

  • Takes additional parameters as query string:
    • ignoreWarnings – If set as true it will exclude zip files that only contain xml files with validation warnings.
    • validationIssues – If set as true will return the zip files that contain xml files with validation issues.
    • xmlErrors – If set as true will return the zip files that contain xml files with xml errors.
  • Filtering will be performed if any of the validationIssuesxmlErrors or ignoreWarnings flags is set as true. If none of them is passed as an argument it will return everything. false values will not effect the result.
  • Procedures/Specimens can be paginated using the query parameters startProcedureCount and resultProcedureSize
    • startProcedureCount – offset
    • resultProcedureSize – max number of results to retrieve
    • Both parameters need to be > 0 or are otherwise ignored
    • By default pagination is enabled default pagination of 1000
  • Example: https://api.mousephenotype.org/tracker/issues/zip/Gmc.2013-08-27.11.impc.zip?ignoreWarnings=true

/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 of the 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 of the 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 of the 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:

IdStatus
1pending
2running
3done
4cancelled
5failed

/pcv/meta/status

Returns a lookup of the xml statuses:

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

/xml/meta/phase

Returns a lookup of the xml phases:

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

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[]

  • Example Link: No real time case present
  • Example Structure :
"validationLogs": [
                    {
                        "message": "'Message for failure",
                        "parameterType": "Parameter Type", 
                        "parameterKey": "Parameter Key",
                        "fatality": "Warning/Error"
                    },
]

The IMPC Newsletter

Get highlights of the most important data releases, news and events, delivered straight to your email inbox

Subscribe to newsletter