Submission Package bug - PT_95S99RWE not in diagnoses manifest

[chris-s-friedman]

Describe the bug

PT_95S99RWE is not in the diagnosis manifest

Expected behavior

PT_95S99RWE should have a diagnosis

Version ID

0.13.0

Effected file(s)

• [ ] sample
• [ ] participant
• [X] diagnosis
• [X] diagnosis_sample_mapping
• [ ] file
• [ ] file_sample_participant_map
• [ ] genomic_info

[chris-s-friedman]

tldr: there are no diagnoses for the event related to the samples for this participant

There are two samples being released in CDS for this participant, BS_KSFM87N1 and BS_YR7Q70YP. Both of these samples are normal samples. They are from sample 7316-65. There are no other aliquots from this sample. Because of this, there are no tumor samples associated with this sample, so, in the histologies file, there is no diagnosis associated with this event. So, there is no diagnosis to associate here.

Unless we use diagnoses from a different event... which breaks our model for where diagnoses come from.

[chris-s-friedman]

there are other diagnoses from the other sample relate to this participant. Excerpt from the histologies file:

Kids_First_Biospecimen_ID	Kids_First_Participant_ID	sample_id	pathology_diagnosis	broad_histology	pathology_free_text_diagnosis	sample_type
BS_9D7YPY72	PT_95S99RWE	7316-323	Craniopharyngioma		craniopharyngioma	Tumor
BS_CV8J6WK8	PT_95S99RWE	7316-323	Craniopharyngioma		craniopharyngioma	Tumor
BS_HYGK88B0	PT_95S99RWE	7316-323	Craniopharyngioma		craniopharyngioma	Tumor
BS_KSFM87N1	PT_95S99RWE	7316-65				Normal
BS_YR7Q70YP	PT_95S99RWE	7316-65				Normal
BS_YS76FT7P	PT_95S99RWE	7316-323	Craniopharyngioma		craniopharyngioma	Tumor