Get associated BAM files

getAssociatedBamfiles

URL

/api/v1/getAssociatedBamfiles

Description

For use with the Ion Reporter™ Server only. Gets the BAM file or files that are associated with a single sample or analysis, or multiple samples or analyses, and downloads the BAM files using the /downloadBAM API call. Returns a JSON response object that contains the BAM file links. After BAM files are displayed as output as JSON, users can download the BAM file using the /api/v1/downloadBAM API call.

Method

GET

Request query parameters

  • name

    String, Mandatory.

    Single/multiple names of either sample or analysis.

  • type

    String. Conditional.

    If the type parameter is not provided, name is considered as analysis name, For sample name(s), type is mandatory (For example, type=sample).

Sample request

https://dev.ionreporter.thermofisher.com/api/v1/getAssociatedBamfiles?name=multi
bam test,Sample_1_v2,test62,1194954B_Bladder_ManLib,Demo AmpliSeq
Exome VCF,invalid_sapmle1,Demo AmpliSeq IDP
Mother&type=sample 
					 

Analysis request

 http://dev.ionreporter.thermofisher.com/api/v1/getAssociatedBamfiles?name=Demo
AmpliSeq IDP
Daughter_1518065163079,invalid_name,trio_c1078_2018-03-01-20-35-30-948

Request headers

Content-Type:application/x-www-form-urlencoded

Authorization:API Token

Returns

Sample Response
[

    {
       "sample": "1194954B_Bladder_ManLib",
        "bam_links": [
            "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/
Zyklus/data/IRU_Uploads/20170727_08_45_03/v1/1194954B_Bladder_ManLib/1_IonXpress_030_R_2016_12_20_13_27_19_user_S5-00105-348-C656s2_OCAv3.4_CNVbaseline_ManLibs_Pool6_chip6_Auto_user_S5-00105-348-C656s2_OCAv3.4_CNVbaseline_ManLibs_Pool6_chip6_1074.bam"
        ]
    },
    {
        "sample": "invalid_sapmle1",
        "bam_links": [
            "Sample or Bam file could not be found for the specified name."
        ]
    },
    {
        "sample": "multi bam test",
        "bam_links": [
            "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/Zyklus/data/IRU_Uploads/2017-12-29_1_51_48/v1/e5272-wfa-l165_v3/rawlib.bam",
            "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/Zyklus/data/IRU_Uploads/20171229_14_54_21/v1/sample_test16/1_IonDx-9_rawlib12.bam"
        ]
    },
    {
        "sample": "Demo AmpliSeq Exome VCF",
        "bam_links": [
            "Sample or Bam file could not be found for the specified name."
        ]
    }
]

Analysis Response

[
    {
        "analysis": "trio_c1078_2018-03-01-20-35-30-948",
        "version": "IR510",
        "analysisStatus": "SUCCESSFUL",
        "sampleDetails": [
            {
                "sampleName": "Demo AmpliSeq IDP Daughter",
                "sampleRole": "proband",
                "inputBam": [
                    "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_daughter.bam"
                ],
                "processedBam": [
                    "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/uattestsskadmuser@gmail.com/Demo_AmpliSeq_IDP_Daughter_Demo_AmpliSeq_IDP_Father_Demo_AmpliSeq_IDP_Mother/Demo_AmpliSeq_IDP_Daughter_20180301150555171/outputs/VariantCallerActorProband-00/merged.bam.ptrim.bam"
                ]
            },
            {
                "sampleName": "Demo AmpliSeq IDP Father",
                "sampleRole": "father",
                "inputBam": [
                    "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_father.bam"
                ],
                "processedBam": [
                    "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/uattestsskadmuser@gmail.com/Demo_AmpliSeq_IDP_Daughter_Demo_AmpliSeq_IDP_Father_Demo_AmpliSeq_IDP_Mother/Demo_AmpliSeq_IDP_Daughter_20180301150555171/outputs/VariantCallerActorFather-00/merged.bam.ptrim.bam"
                ]
            },
            {
                "sampleName": "Demo AmpliSeq IDP Mother",
                "sampleRole": "mother",
                "inputBam": [
                    "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/demodata/PGM/AmpliSeq_IDP/AmpliSeq_IDP_mother.bam"
                ],
                "processedBam": [
                    "http://dev.ionreporter.thermofisher.com:80/api/v1/downloadBAM?filePath=/shared/data/ShazIndia-Labs/uattestsskadmuser@gmail.com/Demo_AmpliSeq_IDP_Daughter_Demo_AmpliSeq_IDP_Father_Demo_AmpliSeq_IDP_Mother/Demo_AmpliSeq_IDP_Daughter_20180301150555171/outputs/VariantCallerActorMother-00/merged.bam.ptrim.bam"

                ]
            }
        ]
    },
    {
        "analysis": "invalid_name",
        "message": "Analysis could not be found for the specified name."
    }
]

Response fields

Status code

Response message

200

Successful response

400

Bad request

404

Not found

401

User is not authenticated

500

Error occurred

Curl commands

curl -X GET -k "http://<your server name>/api/v1/getAssociatedBamfiles?name=multi bam test,Sample_1_v2,
test62,1194954B_Bladder_ManLib,Demo AmpliSeq Exome VCF,invalid_sapmle1,Demo AmpliSeq IDP Mother&type=sample" -H 
"Content-Type:application/x-www-form-urlencoded" -H "Authorization:ODA5YTVlZDcyNjkyNDg5Mjg2YmZiNjI3ODExZWFmM2I3NzhkNzg0MDU5M2U
0YmIxOGU2YjQ2OTRmYmIxZjAxNw"
curl -X GET -k "http://<your server name>/api/v1/getAssociatedBamfiles?name=Demo AmpliSeq IDP 
Daughter_1518065163079,invalid_name,trio_c1078_2018-03-01-20-35-30-948" -H "Content-Type:application/x-www-form-urlencoded" -H 
"Authorization:ODA5YTVlZDcyNjkyNDg5Mjg2YmZiNjI3ODExZWFmM2I3NzhkNzg0MDU5M2U0YmIxOGU2YjQ2OTRmYmIxZjAxNw