🐛 P1000-US donors show incorrect registered samples in dashboard

[edsu7]

Describe the bug

The following query is returned when using the dashboard:

            "entries": [
                {
                    "id": "P1000-US::DO256489",
                    "donorId": "DO256489",
                    "programShortName": "P1000-US",
                    "validWithCurrentDictionary": true,
                    "releaseStatus": "NO_RELEASE",
                    "submitterDonorId": "JVV024",
                    "submittedCoreDataPercent": 1,
                    "registeredNormalSamples": 1,
                    "registeredTumourSamples": 0,
                    "publishedNormalAnalysis": 0,
                    "publishedTumourAnalysis": 0,
                    "alignmentsCompleted": 0,
                    "alignmentsRunning": 0,
                    "alignmentsFailed": 0,
                    "sangerVcsCompleted": 0,
                    "sangerVcsRunning": 0,
                    "sangerVcsFailed": 0,
                    "mutectFailed": 0,
                    "mutectRunning": 0,
                    "mutectCompleted": 0,
                    "openAccessFailed": 0,
                    "openAccessRunning": 0,
                    "openAccessCompleted": 0,
                    "processingStatus": "REGISTERED",
                    "updatedAt": "2024-11-25T21:21:18.667Z",
                    "rnaRegisteredNormalSamples": 0,
                    "rnaRegisteredTumourSamples": 2,
                    "rnaPublishedNormalAnalysis": 0,
                    "rnaPublishedTumourAnalysis": 0,
                    "rnaAlignmentsCompleted": 0,
                    "rnaAlignmentsRunning": 0,
                    "rnaAlignmentFailed": 0,
                    "matchedTNPairsDNA": 0,
                    "__typename": "DonorSummaryEntry"
                }
            ],

Note 2 RNA and 1 DNA

But what is registered is the opposite:

Incorrect status will eventually block data from being released.

Steps To Reproduce

Steps to reproduce the behaviour:

1. Go to P1000-US production dashboard
2. filter for 'DO256489'
3. Note # of sample in DNA tab and RNA tab

Expected behaviour

Results should be 1 RNA and 2 DNA

Additional notes

• Perhaps an elastic search issue?
• 13 donors affected:

DO256475
DO256477
DO256478
DO256479
DO256480
DO256482
DO256484
DO256487
DO256489
DO256491
DO256492
DO256493
DO256494

[edsu7]

Summarizing the convo I had with Ciaran here.

• issue occurs when a specimen has multiple samples of multiple sample types (see example datasets)
• dashboard miscounts one sample type for another, see following examples:
  • data1 (undercount of DNA, overcount of RNA)
    
    
  • data2 (undercount of RNA, overcount of DNA)
    
    
• a theory: the first record for the specimen that appears determines what sample type overcount will be e.g. in data2, the first record is DNA resulting in overcounting all records as DNA

Test datasets used:

• Data1

program_id	submitter_donor_id	gender	submitter_specimen_id	specimen_tissue_source	tumour_normal_designation	specimen_type	submitter_sample_id	sample_type
TEST-CA	JVV020	Female	JVV020-N	Solid tissue	Normal	Normal	JVV020-N-L1-FTHW739	Amplified DNA
TEST-CA	JVV020	Female	JVV020T	Solid tissue	Tumour	Primary tumour	JVV020T-L2-CWFC429	Total RNA
TEST-CA	JVV020	Female	JVV020T	Solid tissue	Tumour	Primary tumour	JVV020T-L1-KIFH238	Amplified DNA

• Data2

program_id	submitter_donor_id	gender	submitter_specimen_id	specimen_tissue_source	tumour_normal_designation	specimen_type	submitter_sample_id	sample_type
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN1	Solid tissue	Normal	Normal	SPECIMEN1-SAMPLE1-DNA1	Amplified DNA
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN1	Solid tissue	Normal	Normal	SPECIMEN1-SAMPLE2-RNA1	Total RNA
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN2	Solid tissue	Tumour	Primary tumour	SPECIMEN2-SAMPLE3-DNA1	Amplified DNA
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN2	Solid tissue	Tumour	Primary tumour	SPECIMEN2-SAMPLE4-DNA2	Amplified DNA
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN2	Solid tissue	Tumour	Primary tumour	SPECIMEN2-SAMPLE5-DNA3	Amplified DNA
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN2	Solid tissue	Tumour	Primary tumour	SPECIMEN2-SAMPLE6-RNA1	Total RNA
TEST-INTL	ANON-DONOR1	Female	DONOR1-SPECIMEN2	Solid tissue	Tumour	Primary tumour	SPECIMEN2-SAMPLE7-RNA2	Total RNA

[ciaranschutte]

Tested both datasets #1198 (comment) and looks good
Please verify @edsu7

will have to update PROD Env vars for ego tokens before deploying @bhavikbhagat93

[edsu7]

Confirmed fix is working on QA