Plannedexperiment Resource¶

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

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

Perform CRUD operations on plannedexperiment 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
planDisplayedName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sequencekitname	Unicode string data. Ex: “Hello World”		true	false	true	false	string
forward3primeadapter	Unicode string data. Ex: “Hello World”		true	false	true	false	string
preAnalysis	Boolean data. Ex: True	false	false	false	true	false	boolean
chipType	Unicode string data. Ex: “Hello World”		false	false	false	false	string
planShortID	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
username	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sampleSetDisplayedName	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
sampleSetGroupType	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
library	Unicode string data. Ex: “Hello World”		true	false	true	false	string
planStatus	Unicode string data. Ex: “Hello World”		false	false	true	false	string
sample	Unicode string data. Ex: “Hello World”		true	false	true	false	string
reverselibrarykey	Unicode string data. Ex: “Hello World”		false	true	false	false	string
storage_options	Unicode string data. Ex: “Hello World”	A	false	false	false	false	string
planName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
planExecutedDate	A date & time as a string. Ex: “2010-11-10T03:07:43”	n/a	true	false	false	false	datetime
samplePrepKitName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
reverse_primer	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
applicationGroup	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
seqKitBarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
id	Integer data. Ex: 2673		false	false	true	true	integer
barcodedSamples	Unicode string data. Ex: “Hello World”		true	false	true	false	string
metaData	Unicode string data. Ex: “Hello World”	{}	false	false	true	false	string
sampleSet_uid	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
isFavorite	Boolean data. Ex: True	false	false	false	true	false	boolean
sampleSet_planIndex	Integer data. Ex: 2673	0	false	false	false	false	integer
barcodeId	Unicode string data. Ex: “Hello World”		true	false	true	false	string
runMode	Unicode string data. Ex: “Hello World”		false	false	true	false	string
regionfile	Unicode string data. Ex: “Hello World”		false	false	true	false	string
isPlanGroup	Boolean data. Ex: True	false	false	false	true	false	boolean
sampleSet_planTotal	Integer data. Ex: 2673	0	false	false	false	false	integer
selectedPlugins	Unicode string data. Ex: “Hello World”		true	false	true	false	string
experiment	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
bedfile	Unicode string data. Ex: “Hello World”		false	false	true	false	string
templatingKitName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
runType	Unicode string data. Ex: “Hello World”	GENS	false	false	false	false	string
templatingKitBarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sampleDisplayedName	Unicode string data. Ex: “Hello World”		true	false	true	false	string
sampleSet	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
planPGM	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
isSystemDefault	Boolean data. Ex: True	false	false	false	true	false	boolean
autoName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
isReusable	Boolean data. Ex: True	false	false	false	true	false	boolean
qcValues	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	true	false	true	false	related
isDuplicateReads	Boolean data. Ex: True	n/a	false	false	false	false	boolean
controlSequencekitname	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
libraryKey	Unicode string data. Ex: “Hello World”		false	false	true	false	string
tfKey	Unicode string data. Ex: “Hello World”		false	false	true	false	string
flows	Integer data. Ex: 2673	0	false	false	false	false	integer
sampleTubeLabel	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
date	A date & time as a string. Ex: “2010-11-10T03:07:43”	n/a	true	false	false	false	datetime
librarykitname	Unicode string data. Ex: “Hello World”		true	false	true	false	string
isSystem	Boolean data. Ex: True	false	false	false	true	false	boolean
libkit	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
projects	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	true	false	true	false	related
variantfrequency	Unicode string data. Ex: “Hello World”		false	true	false	false	string
autoAnalyze	Boolean data. Ex: True	n/a	false	false	false	false	boolean
flowsInOrder	Unicode string data. Ex: “Hello World”		true	false	true	false	string
parentPlan	Unicode string data. Ex: “Hello World”	None	false	false	true	false	string
childPlans	A list of data. Ex: [‘abc’, 26.73, 8]	[]	false	false	false	false	list
pairedEndLibraryAdapterName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
reverse3primeadapter	Unicode string data. Ex: “Hello World”		false	true	false	false	string
adapter	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sampleGrouping	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
irworkflow	Unicode string data. Ex: “Hello World”		false	false	true	false	string
chipBarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
planExecuted	Boolean data. Ex: True	false	false	false	true	false	boolean
project	Unicode string data. Ex: “Hello World”	n/a	false	true	true	false	string
usePostBeadfind	Boolean data. Ex: True	false	false	false	true	false	boolean
storageHost	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
expName	Unicode string data. Ex: “Hello World”		false	false	true	false	string
runname	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
usePreBeadfind	Boolean data. Ex: True	false	false	false	true	false	boolean
planGUID	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
cycles	Integer data. Ex: 2673	n/a	true	false	false	false	integer
notes	Unicode string data. Ex: “Hello World”		true	false	true	false	string
resource_uri	Unicode string data. Ex: “Hello World”	n/a	false	true	false	false	string

Example request¶

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

Python example¶

import requests

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

plannedexperiments = ts_api_response["objects"]

for plannedexperiment in plannedexperiments:
    print plannedexperiment

Torrent Server response¶

{
    "meta": {
        "previous": null,
        "total_count": 4193,
        "offset": 0,
        "limit": 1,
        "next": "/rundb/api/v1/plannedexperiment/?offset=1&limit=1&format=json"
    },
    "objects": [
        {
            "planDisplayedName": "-R185427-in_house-ml",
            "autoAnalyze": true,
            "templatingKitBarcode": null,
            "preAnalysis": true,
            "thumbnailanalysisargs": "",
            "applicationGroup": null,
            "libkit": null,
            "planPGM": null,
            "prebasecallerargs": "BaseCaller --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16 --calibration-training=100000 --flow-signals-type scaled-residual",
            "alignmentargs": "stage1 map4",
            "thumbnailbasecallerargs": "",
            "sampleSet_planTotal": 0,
            "projects": [
                "avalanche"
            ],
            "notes": "1T LLP Pool 2 Lib7679 200bp psp4_test lot131113 in house reagents ",
            "sequencekitname": "",
            "storageHost": null,
            "expName": "",
            "cycles": 250,
            "isReverseRun": false,
            "storage_options": "A",
            "thumbnailalignmentargs": "",
            "chipType": "316v2",
            "library": "hg19",
            "reverselibrarykey": "",
            "planName": "-R185427-in_house-ml",
            "seqKitBarcode": null,
            "barcodeId": "IonXpress",
            "isPlanGroup": false,
            "experiment": "/rundb/api/v1/experiment/12549/",
            "bedfile": "",
            "isReusable": false,
            "isDuplicateReads": false,
            "thumbnailbeadfindargs": "",
            "librarykitname": "",
            "adapter": null,
            "basecallerargs": "BaseCaller --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16",
            "parentPlan": null,
            "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC",
            "planStatus": "planned",
            "samplePrepKitName": null,
            "metaData": {
                "torrenthub.cbd_hub_id": "185427"
            },
            "sampleSet_uid": null,
            "isFavorite": false,
            "sampleSet_planIndex": 0,
            "qcValues": [],
            "analysisargs": "Analysis --from-beadfind",
            "templatingKitName": null,
            "runType": "WGNM",
            "username": "ml",
            "planShortID": "XV5JM",
            "sampleDisplayedName": "",
            "prethumbnailbasecallerargs": "",
            "controlSequencekitname": null,
            "flowsInOrder": "",
            "childPlans": [],
            "pairedEndLibraryAdapterName": null,
            "runMode": "",
            "irworkflow": "",
            "planExecuted": false,
            "project": "avalanche",
            "usePostBeadfind": true,
            "runname": null,
            "planGUID": "4df71954-4746-47e6-ad8b-bd834d005e44",
            "sampleTubeLabel": null,
            "sampleSetGroupType": null,
            "sample": "",
            "planExecutedDate": null,
            "reverse_primer": null,
            "id": 44458,
            "barcodedSamples": {},
            "regionfile": "",
            "selectedPlugins": {
                "pinsPerFlow": {
                    "name": "pinsPerFlow"
                },
                "libClonality": {
                    "name": "libClonality"
                },
                "TestFragmentTorturer": {
                    "name": "TestFragmentTorturer"
                },
                "avalanche_slush_shovel": {
                    "name": "avalanche_slush_shovel"
                },
                "detailedReport": {
                    "name": "detailedReport"
                },
                "bubblePlots": {
                    "name": "bubblePlots"
                },
                "bubbleRun": {
                    "name": "bubbleRun"
                },
                "1_Torrent_Accuracy": {
                    "name": "1_Torrent_Accuracy"
                },
                "ErrByFlow": {
                    "name": "ErrByFlow"
                },
                "variantCaller": {
                    "userInput": {
                        "librarytype": "WGNM",
                        "variationtype": ""
                    },
                    "name": "variantCaller"
                },
                "Reverse_Primer_Lookup": {
                    "name": "Reverse_Primer_Lookup"
                },
                "rawTrace": {
                    "name": "rawTrace"
                },
                "filterAndTrim": {
                    "name": "filterAndTrim"
                },
                "AvgTrace": {
                    "name": "AvgTrace"
                },
                "chipDiagnostics": {
                    "name": "chipDiagnostics"
                },
                "qv_binner": {
                    "name": "qv_binner"
                },
                "spatialPlots": {
                    "name": "spatialPlots"
                },
                "validateVariantCaller": {
                    "userInput": {
                        "truth_major_snp": "TSExomeV2_NA12878_SNPs_Confident.bed",
                        "Region": "Exome",
                        "Sample": "NA12878",
                        "truth_minor_snp": "None",
                        "truth_major_indel": "TSExomeV2_NA12878_Confident_InDels.bed",
                        "truth_minor_indel": "None"
                    },
                    "name": "validateVariantCaller"
                },
                "barcodeMixtureAnalysis": {
                    "name": "barcodeMixtureAnalysis"
                },
                "PerBaseQualEval": {
                    "name": "PerBaseQualEval"
                },
                "z_homopolymerAnalysis": {
                    "name": "z_homopolymerAnalysis"
                },
                "start_point_analysis": {
                    "name": "start_point_analysis"
                },
                "RateMap": {
                    "name": "RateMap"
                },
                "separator": {
                    "name": "separator"
                },
                "GC_seq_performance": {
                    "name": "GC_seq_performance"
                },
                "flowErr": {
                    "name": "flowErr"
                }
            },
            "beadfindargs": "justBeadFind",
            "sampleSet": null,
            "isSystemDefault": false,
            "autoName": null,
            "libraryKey": "TCAG",
            "flows": 1000,
            "date": "2014-01-30T20:25:40.000383+00:00",
            "isSystem": false,
            "variantfrequency": "",
            "sampleSetDisplayedName": "",
            "tfKey": "",
            "sampleGrouping": null,
            "chipBarcode": null,
            "usePreBeadfind": true,
            "resource_uri": "/rundb/api/v1/plannedexperiment/44458/",
            "reverse3primeadapter": ""
        }
    ]
}

Allowed HTTP methods¶

get
post
put
delete
patch

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