Experiment Resource¶

Resource URL: http://mytorrentserver/rundb/api/v1/experiment/

Schema URL: http://mytorrentserver/rundb/api/v1/experiment/schema/

Perform CRUD operations on experiment resources and data elements.

Fields table¶

field	help text	default	nullable	readonly	blank	unique	type
isReverseRun	Boolean data. Ex: True	false	false	false	true	false	boolean
storage_options	Unicode string data. Ex: “Hello World”	A	false	false	false	false	string
chipType	Unicode string data. Ex: “Hello World”	n/a	false	false	false	false	string
user_ack	Unicode string data. Ex: “Hello World”	U	false	false	false	false	string
results	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	false	false	false	false	related
sample	Unicode string data. Ex: “Hello World”	n/a	false	true	true	false	string
runMode	Unicode string data. Ex: “Hello World”		false	false	true	false	string
reverse_primer	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
seqKitBarcode	Unicode string data. Ex: “Hello World”		false	false	true	false	string
id	Integer data. Ex: 2673		false	false	true	true	integer
metaData	Unicode string data. Ex: “Hello World”	{}	false	false	true	false	string
log	Unicode string data. Ex: “Hello World”	{}	false	false	true	false	string
sequencekitbarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
resource_uri	Unicode string data. Ex: “Hello World”	n/a	false	true	false	false	string
eas_set	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	true	false	true	false	related
runtype	Unicode string data. Ex: “Hello World”	n/a	false	false	false	false	string
platform	Unicode string data. Ex: “Hello World”		false	false	true	false	string
samples	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	true	false	true	false	related
pinnedRepResult	Boolean data. Ex: True	false	false	false	true	false	boolean
reagentBarcode	Unicode string data. Ex: “Hello World”		false	false	true	false	string
star	Boolean data. Ex: True	false	false	false	true	false	boolean
isProton	Unicode string data. Ex: “Hello World”	n/a	false	true	false	false	string
expCompInfo	Unicode string data. Ex: “Hello World”		false	false	true	false	string
resultDate	A date & time as a string. Ex: “2010-11-10T03:07:43”	true	true	false	false	false	datetime
flows	Integer data. Ex: 2673	n/a	false	false	false	false	integer
plan	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
date	A date & time as a string. Ex: “2010-11-10T03:07:43”	n/a	false	false	false	false	datetime
diskusage	Integer data. Ex: 2673	n/a	true	false	false	false	integer
unique	Unicode string data. Ex: “Hello World”	n/a	false	false	false	true	string
expDir	Unicode string data. Ex: “Hello World”	n/a	false	false	false	false	string
autoAnalyze	Boolean data. Ex: True	true	false	false	true	false	boolean
ftpStatus	Unicode string data. Ex: “Hello World”		false	false	true	false	string
flowsInOrder	Unicode string data. Ex: “Hello World”		false	false	true	false	string
baselineRun	Boolean data. Ex: True	false	false	false	true	false	boolean
displayName	Unicode string data. Ex: “Hello World”		false	false	false	false	string
notes	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sequencekitname	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
chipBarcode	Unicode string data. Ex: “Hello World”		false	false	true	false	string
pgmName	Unicode string data. Ex: “Hello World”	n/a	false	false	false	false	string
storageHost	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
expName	Unicode string data. Ex: “Hello World”	n/a	false	false	false	false	string
status	Unicode string data. Ex: “Hello World”		false	false	true	false	string
usePreBeadfind	Boolean data. Ex: True	true	false	false	true	false	boolean
cycles	Integer data. Ex: 2673	n/a	false	false	false	false	integer
rawdatastyle	Unicode string data. Ex: “Hello World”	single	true	false	false	false	string

Example request¶

Request URL: http://mytorrentserver/rundb/api/v1/experiment/?format=json&limit=1

Python example¶

import requests

ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/experiment/", params={"format": "json", "limit": 1})
ts_api_response = ts_api_request.json()

experiments = ts_api_response["objects"]

for experiment in experiments:
    print experiment

Torrent Server response¶

{
    "meta": {
        "previous": null,
        "total_count": 21008,
        "offset": 0,
        "limit": 1,
        "next": "/rundb/api/v1/experiment/?offset=1&limit=1&format=json"
    },
    "objects": [
        {
            "isReverseRun": false,
            "storage_options": "A",
            "chipType": "",
            "user_ack": "U",
            "results": [],
            "sample": "E115943-lq204-01-L8095",
            "runMode": "",
            "reverse_primer": null,
            "seqKitBarcode": "",
            "id": 10132,
            "metaData": {},
            "log": {},
            "sequencekitbarcode": "",
            "resource_uri": "/rundb/api/v1/experiment/10132/",
            "eas_set": [
                {
                    "isEditable": true,
                    "hotSpotRegionBedFile": "",
                    "results": [],
                    "targetRegionBedFile": "/results/uploads/BED/19/hg19/unmerged/detail/Ion-TargetSeq-Exome-50Mb-hg19_revA.bed",
                    "thumbnailalignmentargs": "",
                    "thumbnailanalysisargs": "",
                    "id": 10575,
                    "barcodedSamples": {},
                    "reference": "hg19",
                    "isOneTimeOverride": false,
                    "analysisargs": "",
                    "thumbnailcalibrateargs": "",
                    "realign": false,
                    "selectedPlugins": {
                        "pinsPerFlow": {
                            "name": "pinsPerFlow"
                        },
                        "duplicateReads_useZC": {
                            "name": "duplicateReads_useZC"
                        },
                        "libClonality": {
                            "name": "libClonality"
                        },
                        "ProtonErrors": {
                            "name": "ProtonErrors"
                        },
                        "PhasingReport": {
                            "name": "PhasingReport"
                        },
                        "detailedReport": {
                            "name": "detailedReport"
                        },
                        "extended_chip_check": {
                            "name": "extended_chip_check"
                        },
                        "1_Torrent_Accuracy": {
                            "name": "1_Torrent_Accuracy"
                        },
                        "ConversionRate": {
                            "name": "ConversionRate"
                        },
                        "rawTrace": {
                            "name": "rawTrace"
                        },
                        "filterAndTrim": {
                            "name": "filterAndTrim"
                        },
                        "fsRecalibration": {
                            "name": "fsRecalibration"
                        },
                        "timingPerformance": {
                            "name": "timingPerformance"
                        },
                        "NucRiseParams": {
                            "name": "NucRiseParams"
                        },
                        "AvgTrace": {
                            "name": "AvgTrace"
                        },
                        "autoCal": {
                            "name": "autoCal"
                        },
                        "flowCell": {
                            "name": "flowCell"
                        },
                        "chipDiagnostics": {
                            "name": "chipDiagnostics"
                        },
                        "rawPlots": {
                            "name": "rawPlots"
                        },
                        "spatialPlots": {
                            "name": "spatialPlots"
                        },
                        "RateMapEDA": {
                            "name": "RateMapEDA"
                        },
                        "barcodeMixtureAnalysis": {
                            "name": "barcodeMixtureAnalysis"
                        },
                        "z_homopolymerAnalysis": {
                            "name": "z_homopolymerAnalysis"
                        },
                        "separator": {
                            "name": "separator"
                        },
                        "GC_seq_performance": {
                            "name": "GC_seq_performance"
                        },
                        "flowErr": {
                            "name": "flowErr"
                        }
                    },
                    "experiment": "/rundb/api/v1/experiment/10132/",
                    "barcodeKitName": "",
                    "beadfindargs": "",
                    "threePrimeAdapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC",
                    "thumbnailbasecallerargs": "",
                    "status": "planned",
                    "prebasecallerargs": "",
                    "prethumbnailbasecallerargs": "",
                    "alignmentargs": "",
                    "isDuplicateReads": false,
                    "libraryKey": "TCAG",
                    "date": "2013-05-15T18:30:24.000115+00:00",
                    "libraryKitName": "",
                    "thumbnailbeadfindargs": "",
                    "calibrateargs": "",
                    "tfKey": "",
                    "libraryKitBarcode": null,
                    "base_recalibrate": true,
                    "basecallerargs": "",
                    "resource_uri": "/rundb/api/v1/experimentanalysissettings/10575/"
                }
            ],
            "runtype": "GENS",
            "platform": "PGM",
            "samples": [
                {
                    "status": "run",
                    "sampleSets": [],
                    "description": null,
                    "displayedName": "E115943-lq204-01-L8095",
                    "experiments": [
                        "/rundb/api/v1/experiment/10142/",
                        "/rundb/api/v1/experiment/10132/"
                    ],
                    "externalId": "",
                    "date": "2013-05-15T18:30:24.000176+00:00",
                    "resource_uri": "/rundb/api/v1/sample/2379/",
                    "id": 2379,
                    "name": "E115943-lq204-01-L8095"
                }
            ],
            "pinnedRepResult": false,
            "reagentBarcode": "",
            "star": false,
            "isProton": "False",
            "expCompInfo": "",
            "resultDate": "2013-05-15T18:30:24.000171+00:00",
            "flows": 400,
            "plan": "/rundb/api/v1/plannedexperiment/88364/",
            "date": "2013-05-15T18:30:24.000167+00:00",
            "diskusage": null,
            "unique": "ea5aefc7-e1ec-4c79-9843-b0e299253a9a",
            "expDir": "",
            "autoAnalyze": true,
            "ftpStatus": "Complete",
            "flowsInOrder": "",
            "baselineRun": false,
            "displayName": "ea5aefc7-e1ec-4c79-9843-b0e299253a9a",
            "notes": "OT2 lq204_01 Lib8095 275bp lr2 4B bead 1.2B lib SDS_10mMEDTA break ",
            "sequencekitname": "",
            "chipBarcode": "",
            "pgmName": "",
            "storageHost": null,
            "expName": "ea5aefc7-e1ec-4c79-9843-b0e299253a9a",
            "status": "planned",
            "usePreBeadfind": false,
            "cycles": 0,
            "rawdatastyle": "single"
        }
    ]
}

Allowed HTTP methods¶

get
post
put
delete
patch

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