Planned Experiment Resource¶
Resource URL
http://mytorrentserver/rundb/api/v1/plannedexperiment/Schema URL
http://mytorrentserver/rundb/api/v1/plannedexperiment/schema/Resource Fields¶
| field | help text | default | nullable | readonly | blank | unique | type |
|---|---|---|---|---|---|---|---|
| planDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| autoAnalyze | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| endBarcodeKitName | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| templatingKitBarcode | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| preAnalysis | Boolean data. Ex: True | true | false | false | true | false | boolean |
| applicationGroup | A single related resource. Can be either a URI or set of nested resource data. | n/a | true | false | true | false | related |
| mixedTypeRNA_hotSpotRegionBedFile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| mixedTypeRNA_targetRegionBedFile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| platform | Unicode string data. Ex: “Hello World” | n/a | true | false | true | false | string |
| categories | Unicode string data. Ex: “Hello World” | true | false | false | false | string | |
| planPGM | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| 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 |
| notes | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| sequencekitname | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| base_recalibration_mode | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| 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 | |
| cycles | Integer data. Ex: 2673 | n/a | true | false | false | false | integer |
| 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” | false | false | false | false | string | |
| library | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| reverselibrarykey | Unicode string data. Ex: “Hello World” | false | true | false | false | string | |
| sampleTubeLabel | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| seqKitBarcode | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| barcodeId | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| isPlanGroup | Boolean data. Ex: True | false | false | false | true | false | boolean |
| realign | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| sampleGroupingName | Unicode string data. Ex: “Hello World” | n/a | true | true | 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 | |
| applicationCategoryDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| isReusable | Boolean data. Ex: True | false | false | false | true | false | boolean |
| isDuplicateReads | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| sampleSets | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | true | false | true | false | related |
| librarykitname | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| sseBedFile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| adapter | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| earlyDatFileDeletion | Boolean data. Ex: True | false | false | true | false | false | boolean |
| parentPlan | Unicode string data. Ex: “Hello World” | None | false | false | true | false | string |
| origin | Unicode string data. Ex: “Hello World” | true | false | false | false | string | |
| forward3primeadapter | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| isCustom_kitSettings | Boolean data. Ex: True | false | false | false | true | false | boolean |
| samplePrepKitName | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| applicationGroupDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| metaData | Unicode string data. Ex: “Hello World” | {} | false | false | true | false | string |
| isFavorite | 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 |
| planStatus | 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 |
| username | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| planName | 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 | |
| controlSequencekitname | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| tfKey | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| mixedTypeRNA_reference | Unicode string data. Ex: “Hello World” | true | 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 |
| runMode | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| irworkflow | Unicode string data. Ex: “Hello World” | false | false | true | 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 | true | false | false | true | false | boolean |
| libraryReadLength | Integer data. Ex: 2673 | 0 | false | false | false | false | integer |
| runname | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| chefInfo | A dictionary of data. Ex: {‘price’: 26.73, ‘name’: ‘Daniel’} | {} | false | false | false | false | dict |
| planGUID | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| samplePrepProtocol | Unicode string data. Ex: “Hello World” | true | false | false | false | string | |
| planShortID | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| sample | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| planExecutedDate | A date & time as a string. Ex: “2010-11-10T03:07:43” | n/a | true | false | false | false | datetime |
| reverse_primer | 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 | |
| regionfile | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| selectedPlugins | Unicode string data. Ex: “Hello World” | true | false | true | 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 |
| libraryKey | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| flows | Integer data. Ex: 2673 | 0 | false | false | false | false | integer |
| date | A date & time as a string. Ex: “2010-11-10T03:07:43” | n/a | true | false | false | false | datetime |
| isSystem | Boolean data. Ex: True | false | false | false | true | false | boolean |
| variantfrequency | Unicode string data. Ex: “Hello World” | false | true | false | false | string | |
| sampleSetDisplayedName | Unicode string data. Ex: “Hello World” | n/a | true | true | true | false | string |
| flowsInOrder | Unicode string data. Ex: “Hello World” | true | false | true | false | string | |
| libraryPrepType | Unicode string data. Ex: “Hello World” | true | true | true | 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 |
| chipBarcode | Unicode string data. Ex: “Hello World” | false | false | false | false | string | |
| usePreBeadfind | Boolean data. Ex: True | true | false | false | true | false | boolean |
| resource_uri | Unicode string data. Ex: “Hello World” | n/a | false | true | false | false | string |
| libraryPrepTypeDisplayedName | Unicode string data. Ex: “Hello World” | true | true | true | false | string | |
| reverse3primeadapter | Unicode string data. Ex: “Hello World” | false | true | false | false | string |
Example Response¶
{
"meta": {
"previous": null,
"total_count": 111,
"offset": 0,
"limit": 1,
"next": "/rundb/api/v1/plannedexperiment/?offset=1&limit=1&format=json"
},
"objects": [
{
"planDisplayedName": "Ion AmpliSeq HD for Tumor - DNA",
"autoAnalyze": true,
"endBarcodeKitName": "",
"templatingKitBarcode": null,
"preAnalysis": true,
"thumbnailanalysisargs": "Analysis --args-json /opt/ion/config/args_540_analysis.json --thumbnail true",
"applicationGroup": "/rundb/api/v1/applicationgroup/1/",
"mixedTypeRNA_hotSpotRegionBedFile": "",
"mixedTypeRNA_targetRegionBedFile": "",
"platform": "",
"categories": "onco_solidTumor;onco_heme;",
"planPGM": null,
"prebasecallerargs": "BaseCaller --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --wells-normalization on --read-structure AmpliseqHD --tag-filter-method need-prefix",
"alignmentargs": "tmap mapall -g 0 ... --context stage1 map4",
"thumbnailbasecallerargs": "BaseCaller --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on --read-structure AmpliseqHD",
"libkit": null,
"projects": [],
"notes": "",
"sequencekitname": "Ion S5 Sequencing Kit",
"base_recalibration_mode": "standard_recal",
"storageHost": null,
"expName": "",
"thumbnailionstatsargs": "ionstats alignment",
"cycles": null,
"isReverseRun": false,
"storage_options": "A",
"thumbnailalignmentargs": "tmap mapall -g 0 ... --context stage1 map4",
"chipType": "540",
"library": "hg19",
"runMode": "single",
"sampleTubeLabel": "",
"seqKitBarcode": null,
"barcodeId": "Ion AmpliSeq HD Dual Barcode Kit 1-24",
"isPlanGroup": false,
"realign": false,
"sampleGroupingName": "Self",
"experiment": "/rundb/api/v1/experiment/136/",
"bedfile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"applicationCategoryDisplayedName": "Oncology - Solid Tumor | Oncology - HemeOnc",
"isReusable": false,
"isDuplicateReads": false,
"sampleSets": [],
"thumbnailbeadfindargs": "justBeadFind --args-json /opt/ion/config/args_540_beadfind.json --thumbnail true",
"librarykitname": "Ion AmpliSeq HD Library Kit",
"sseBedFile": "",
"adapter": null,
"basecallerargs": "BaseCaller --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --max-phasing-levels 2 --num-unfiltered 1000 --barcode-filter-postpone 1 --wells-normalization on --read-structure AmpliseqHD",
"earlyDatFileDeletion": false,
"parentPlan": null,
"origin": "gui|5.10.0.RC4",
"forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC",
"planStatus": "pending",
"isCustom_kitSettings": false,
"samplePrepKitName": null,
"applicationGroupDisplayedName": "DNA",
"metaData": {
"fromTemplate": "Ion_AmpliSeq_HD_for_Tumor_-_DNA",
"fromTemplateSource": "ION"
},
"isFavorite": false,
"qcValues": [
{
"threshold": 30,
"plannedExperiment": "/rundb/api/v1/plannedexperiment/143/",
"id": 407,
"qcType": {
"description": "",
"minThreshold": 1,
"maxThreshold": 100,
"defaultThreshold": 30,
"qcName": "Key Signal (1-100)",
"id": 2,
"resource_uri": "/rundb/api/v1/qctype/2/"
},
"resource_uri": "/rundb/api/v1/plannedexperimentqc/407/"
},
{
"threshold": 30,
"plannedExperiment": "/rundb/api/v1/plannedexperiment/143/",
"id": 408,
"qcType": {
"description": "",
"minThreshold": 0,
"maxThreshold": 100,
"defaultThreshold": 30,
"qcName": "Usable Sequence (%)",
"id": 3,
"resource_uri": "/rundb/api/v1/qctype/3/"
},
"resource_uri": "/rundb/api/v1/plannedexperimentqc/408/"
},
{
"threshold": 30,
"plannedExperiment": "/rundb/api/v1/plannedexperiment/143/",
"id": 406,
"qcType": {
"description": "",
"minThreshold": 0,
"maxThreshold": 100,
"defaultThreshold": 30,
"qcName": "Bead Loading (%)",
"id": 1,
"resource_uri": "/rundb/api/v1/qctype/1/"
},
"resource_uri": "/rundb/api/v1/plannedexperimentqc/406/"
}
],
"analysisargs": "Analysis --args-json /opt/ion/config/args_540_analysis.json",
"thumbnailcalibrateargs": "Calibration",
"templatingKitName": "Ion Chef S540 V1",
"runType": "AMPS_HD_DNA",
"username": "ionadmin",
"planShortID": "SP1XE",
"sampleDisplayedName": "",
"prethumbnailbasecallerargs": "BaseCaller --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --wells-normalization on --read-structure AmpliseqHD --tag-filter-method need-prefix",
"controlSequencekitname": null,
"tfKey": "ATCG",
"mixedTypeRNA_reference": "",
"childPlans": [],
"pairedEndLibraryAdapterName": "",
"reverselibrarykey": "",
"irworkflow": "",
"planExecuted": false,
"project": "",
"usePostBeadfind": false,
"libraryReadLength": 200,
"runname": null,
"chefInfo": {},
"planGUID": "1d75abf5-4d15-43f5-bb08-1c89d7344175",
"ionstatsargs": "ionstats alignment",
"samplePrepProtocol": "",
"sample": "",
"planExecutedDate": null,
"reverse_primer": null,
"id": 143,
"barcodedSamples": {
"Sample 10": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0110": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0110"
]
},
"Sample 8": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0108": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0108"
]
},
"Sample 9": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0109": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0109"
]
},
"Sample 6": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0106": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0106"
]
},
"Sample 7": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0107": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0107"
]
},
"Sample 4": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0104": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0104"
]
},
"Sample 5": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0105": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0105"
]
},
"Sample 2": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0102": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0102"
]
},
"Sample 3": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0103": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0103"
]
},
"Sample 1": {
"dualBarcodes": [],
"barcodeSampleInfo": {
"IonHDdual_0101": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/2/hg19/unmerged/detail/AmpliSeqExome.20141113.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": "",
"endBarcode": "",
"controlType": "",
"sseBedFile": ""
}
},
"barcodes": [
"IonHDdual_0101"
]
}
},
"custom_args": false,
"regionfile": "",
"selectedPlugins": {
"coverageAnalysis": {
"userInput": {},
"version": "5.8.0.8",
"features": [],
"name": "coverageAnalysis",
"id": 41
},
"variantCaller": {
"userInput": {
"meta": {
"configuration": "ampliseq_hd_ffpe"
}
},
"version": "5.8.0.19",
"features": [],
"name": "variantCaller",
"id": 36
}
},
"beadfindargs": "justBeadFind --args-json /opt/ion/config/args_540_beadfind.json",
"isSystemDefault": false,
"autoName": null,
"libraryKey": "TCAG",
"flows": 500,
"date": "2018-04-13T22:17:13.000108+00:00",
"isSystem": false,
"variantfrequency": "",
"planName": "Ion_AmpliSeq_HD_for_Tumor_-_DNA",
"calibrateargs": "Calibration",
"flowsInOrder": "",
"libraryPrepType": "",
"sampleGrouping": "/rundb/api/v1/samplegrouptype_cv/2/",
"chipBarcode": "",
"sampleSetDisplayedName": "",
"usePreBeadfind": true,
"resource_uri": "/rundb/api/v1/plannedexperiment/143/",
"libraryPrepTypeDisplayedName": "",
"reverse3primeadapter": ""
}
]
}
Allowed list HTTP methods¶
- GET
- POST
- PUT
- DELETE
- PATCH
Allowed detail HTTP methods¶
- GET
- POST
- PUT
- DELETE
- PATCH