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Repository for tracking uncategorizable issues related to backend pipelines work
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Investigate missing IMPACT patient/sample data #1331

Open n1zea144 opened 3 weeks ago

n1zea144 commented 3 weeks ago

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

Understand why and possible recover 116 patients whose data has failed to be imported after requeue. The data was requeued in the afternoon of June 6 and should have been available on June 7.

Technical Description (How are we going to achieve the above)

The following 116 patient data is not in the cBioPortal after a requeue by the CVR team. Are these VIP patients or is something else preventing them from being imported?

P-0003288, P-0006119, P-0011588, P-0013827, P-0014773, P-0014831, P-0017283, P-0019219, P-0024116, P-0025776, P-0026507, P-0028566, P-0031037, P-0031876, P-0032217, P-0033801, P-0035828, P-0036404, P-0036528, P-0038284, P-0038988, P-0039073, P-0039577, P-0044079, P-0045591, P-0045745, P-0046691, P-0047440, P-0047569, P-0047793, P-0047825, P-0048832, P-0048863, P-0051371, P-0053750, P-0053775, P-0056206, P-0056207, P-0060664, P-0061350, P-0061576, P-0062708, P-0062756, P-0065440, P-0066643, P-0066647, P-0066648, P-0066650, P-0066652, P-0066653, P-0066981, P-0069270, P-0070493, P-0070731, P-0070767, P-0070823, P-0071232, P-0071367, P-0071467, P-0071635, P-0071786, P-0071886, P-0072032, P-0072501, P-0072547, P-0074271, P-0074484, P-0074698, P-0075138, P-0075188, P-0076386, P-0076972, P-0077049, P-0077449, P-0077571, P-0077646, P-0077811, P-0078146, P-0078740, P-0078848, P-0079000, P-0079001, P-0079153, P-0079174, P-0079249, P-0079257, P-0079430, P-0079469, P-0079680, P-0080228, P-0080661, P-0081126, P-0081140, P-0081159, P-0081202, P-0081392, P-0081401, P-0081456, P-0082639, P-0082801, P-0082837, P-0082880, P-0083034, P-0083257, P-0083300, P-0083460, P-0083476, P-0085027, P-0085158, P-0085761, P-0086773, P-0090694, P-0090837, P-0092694, P-0093156, P-0095228

Potential Issues

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Technical Requirements

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averyniceday commented 1 day ago

Need more information from Mihir about specific samples --

Using a grep across a couple random points in git history show there are some patients with samples in the history that are not longer present -- trying to requeue results in failure to requeue/not in masterlist. Potentially removed?

Couple cases where couldn't find an exact sample, ran a check in DDP - there are also cases where the patient is not in DDP. Not sure if this is a valid check