360607541994aa88b49fc241c34bd964a1db7b50 lrnassar Tue Sep 29 15:07:07 2026 -0700 Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344 diff --git src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberSamples.tsv src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberSamples.tsv new file mode 100644 index 00000000000..0a581053590 --- /dev/null +++ src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberSamples.tsv @@ -0,0 +1,325 @@ +# Sample list for the hs1 sgdpCopyNumber track, frozen from the 2022 trackDb. +# legacyTrackName is the pre-facet subtrack name; its <region>_<population>_ prefix +# is the only record of region and population for samples the SGDP sample table +# does not cover. Generated once and checked in on purpose: the build script must +# not read the trackDb file it writes. +#libId legacyTrackName bigDataUrl +LP6005441-DNA_A01 EUR_Adygei_LP6005441-DNA_A01_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A01_wssd.bb +LP6005441-DNA_A03 OCN_Bougainville_LP6005441-DNA_A03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A03_wssd.bb +LP6005441-DNA_A04 AMR_Piapoco_LP6005441-DNA_A04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A04_wssd.bb +LP6005441-DNA_A05 EUR_French_LP6005441-DNA_A05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A05_wssd.bb +LP6005441-DNA_A06 EUR_Bergamo_LP6005441-DNA_A06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A06_wssd.bb +LP6005441-DNA_A08 AFR_Mbuti_LP6005441-DNA_A08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A08_wssd.bb +LP6005441-DNA_A09 EAS_Naxi_LP6005441-DNA_A09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A09_wssd.bb +LP6005441-DNA_A10 OCN_Papuan_LP6005441-DNA_A10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A10_wssd.bb +LP6005441-DNA_A11 AFR_Ju_hoan_North_LP6005441-DNA_A11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A11_wssd.bb +LP6005441-DNA_A12 AMR_Surui_LP6005441-DNA_A12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_A12_wssd.bb +LP6005441-DNA_B01 EUR_Adygei_LP6005441-DNA_B01_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B01_wssd.bb +LP6005441-DNA_B02 AFR_BantuKenya_LP6005441-DNA_B02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B02_wssd.bb +LP6005441-DNA_B03 OCN_Bougainville_LP6005441-DNA_B03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B03_wssd.bb +LP6005441-DNA_B04 AMR_Piapoco_LP6005441-DNA_B04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B04_wssd.bb +LP6005441-DNA_B05 EUR_French_LP6005441-DNA_B05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B05_wssd.bb +LP6005441-DNA_B06 EUR_Bergamo_LP6005441-DNA_B06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B06_wssd.bb +LP6005441-DNA_B07 EAS_Lahu_LP6005441-DNA_B07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B07_wssd.bb +LP6005441-DNA_B08 AFR_Mbuti_LP6005441-DNA_B08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B08_wssd.bb +LP6005441-DNA_B09 EAS_Naxi_LP6005441-DNA_B09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B09_wssd.bb +LP6005441-DNA_B10 OCN_Papuan_LP6005441-DNA_B10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B10_wssd.bb +LP6005441-DNA_B11 AFR_Ju_hoan_North_LP6005441-DNA_B11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B11_wssd.bb +LP6005441-DNA_B12 AMR_Surui_LP6005441-DNA_B12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_B12_wssd.bb +LP6005441-DNA_C02 EUR_Basque_LP6005441-DNA_C02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C02_wssd.bb +LP6005441-DNA_C03 SAS_Brahui_LP6005441-DNA_C03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C03_wssd.bb +LP6005441-DNA_C05 EAS_Han_LP6005441-DNA_C05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C05_wssd.bb +LP6005441-DNA_C06 EAS_Japanese_LP6005441-DNA_C06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C06_wssd.bb +LP6005441-DNA_C07 SAS_Makrani_LP6005441-DNA_C07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C07_wssd.bb +LP6005441-DNA_C08 EAS_Miao_LP6005441-DNA_C08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C08_wssd.bb +LP6005441-DNA_C09 EUR_Orcadian_LP6005441-DNA_C09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C09_wssd.bb +LP6005441-DNA_C10 SAS_Pathan_LP6005441-DNA_C10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C10_wssd.bb +LP6005441-DNA_C11 EUR_Sardinian_LP6005441-DNA_C11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_C11_wssd.bb +LP6005441-DNA_D01 SAS_Balochi_LP6005441-DNA_D01_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D01_wssd.bb +LP6005441-DNA_D02 EUR_Basque_LP6005441-DNA_D02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D02_wssd.bb +LP6005441-DNA_D03 SAS_Brahui_LP6005441-DNA_D03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D03_wssd.bb +LP6005441-DNA_D04 EAS_Dai_LP6005441-DNA_D04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D04_wssd.bb +LP6005441-DNA_D05 EAS_Han_LP6005441-DNA_D05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D05_wssd.bb +LP6005441-DNA_D06 EAS_Japanese_LP6005441-DNA_D06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D06_wssd.bb +LP6005441-DNA_D07 SAS_Makrani_LP6005441-DNA_D07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D07_wssd.bb +LP6005441-DNA_D08 EAS_Miao_LP6005441-DNA_D08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D08_wssd.bb +LP6005441-DNA_D09 EUR_Orcadian_LP6005441-DNA_D09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D09_wssd.bb +LP6005441-DNA_D10 SAS_Pathan_LP6005441-DNA_D10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D10_wssd.bb +LP6005441-DNA_D11 EUR_Sardinian_LP6005441-DNA_D11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D11_wssd.bb +LP6005441-DNA_D12 EAS_Tu_LP6005441-DNA_D12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_D12_wssd.bb +LP6005441-DNA_E02 EUR_BedouinB_LP6005441-DNA_E02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E02_wssd.bb +LP6005441-DNA_E03 SAS_Burusho_LP6005441-DNA_E03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E03_wssd.bb +LP6005441-DNA_E05 SAS_Hazara_LP6005441-DNA_E05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E05_wssd.bb +LP6005441-DNA_E06 SAS_Kalash_LP6005441-DNA_E06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E06_wssd.bb +LP6005441-DNA_E07 AFR_Mandenka_LP6005441-DNA_E07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E07_wssd.bb +LP6005441-DNA_E08 SIB_Mongola_LP6005441-DNA_E08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E08_wssd.bb +LP6005441-DNA_E09 EAS_Oroqen_LP6005441-DNA_E09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E09_wssd.bb +LP6005441-DNA_E10 AMR_Pima_LP6005441-DNA_E10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_E10_wssd.bb +LP6005441-DNA_F01 AFR_BantuHerero_LP6005441-DNA_F01_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F01_wssd.bb +LP6005441-DNA_F02 EUR_BedouinB_LP6005441-DNA_F02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F02_wssd.bb +LP6005441-DNA_F03 SAS_Burusho_LP6005441-DNA_F03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F03_wssd.bb +LP6005441-DNA_F04 EAS_Daur_LP6005441-DNA_F04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F04_wssd.bb +LP6005441-DNA_F05 SAS_Hazara_LP6005441-DNA_F05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F05_wssd.bb +LP6005441-DNA_F06 SAS_Kalash_LP6005441-DNA_F06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F06_wssd.bb +LP6005441-DNA_F07 AFR_Mandenka_LP6005441-DNA_F07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F07_wssd.bb +LP6005441-DNA_F08 SIB_Mongola_LP6005441-DNA_F08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F08_wssd.bb +LP6005441-DNA_F09 EAS_Oroqen_LP6005441-DNA_F09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F09_wssd.bb +LP6005441-DNA_F10 AMR_Pima_LP6005441-DNA_F10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F10_wssd.bb +LP6005441-DNA_F12 EAS_Tujia_LP6005441-DNA_F12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_F12_wssd.bb +LP6005441-DNA_G02 AFR_Biaka_LP6005441-DNA_G02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G02_wssd.bb +LP6005441-DNA_G03 EAS_Cambodian_LP6005441-DNA_G03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G03_wssd.bb +LP6005441-DNA_G04 EUR_Druze_LP6005441-DNA_G04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G04_wssd.bb +LP6005441-DNA_G05 EAS_Hezhen_LP6005441-DNA_G05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G05_wssd.bb +LP6005441-DNA_G06 AMR_Karitiana_LP6005441-DNA_G06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G06_wssd.bb +LP6005441-DNA_G07 AMR_Mayan_LP6005441-DNA_G07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G07_wssd.bb +LP6005441-DNA_G08 AFR_Mozabite_LP6005441-DNA_G08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G08_wssd.bb +LP6005441-DNA_G09 EUR_Palestinian_LP6005441-DNA_G09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G09_wssd.bb +LP6005441-DNA_G10 EUR_Russian_LP6005441-DNA_G10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G10_wssd.bb +LP6005441-DNA_G11 SAS_Sindhi_LP6005441-DNA_G11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G11_wssd.bb +LP6005441-DNA_G12 EUR_Tuscan_LP6005441-DNA_G12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_G12_wssd.bb +LP6005441-DNA_H02 AFR_Biaka_LP6005441-DNA_H02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H02_wssd.bb +LP6005441-DNA_H03 EAS_Cambodian_LP6005441-DNA_H03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H03_wssd.bb +LP6005441-DNA_H05 EAS_Hezhen_LP6005441-DNA_H05_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H05_wssd.bb +LP6005441-DNA_H06 AMR_Karitiana_LP6005441-DNA_H06_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H06_wssd.bb +LP6005441-DNA_H07 AMR_Mayan_LP6005441-DNA_H07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H07_wssd.bb +LP6005441-DNA_H08 AFR_Mozabite_LP6005441-DNA_H08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H08_wssd.bb +LP6005441-DNA_H09 EUR_Palestinian_LP6005441-DNA_H09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H09_wssd.bb +LP6005441-DNA_H10 EUR_Russian_LP6005441-DNA_H10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H10_wssd.bb +LP6005441-DNA_H11 SAS_Sindhi_LP6005441-DNA_H11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H11_wssd.bb +LP6005441-DNA_H12 EUR_Tuscan_LP6005441-DNA_H12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005441-DNA_H12_wssd.bb +LP6005442-DNA_A02 AFR_Yoruba_LP6005442-DNA_A02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A02_wssd.bb +LP6005442-DNA_A03 EUR_Bulgarian_LP6005442-DNA_A03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A03_wssd.bb +LP6005442-DNA_A04 EUR_Georgian_LP6005442-DNA_A04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A04_wssd.bb +LP6005442-DNA_A08 EUR_Hungarian_LP6005442-DNA_A08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A08_wssd.bb +LP6005442-DNA_A09 OCN_Australian_LP6005442-DNA_A09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A09_wssd.bb +LP6005442-DNA_A10 AFR_Esan_LP6005442-DNA_A10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A10_wssd.bb +LP6005442-DNA_A11 EUR_Spanish_LP6005442-DNA_A11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A11_wssd.bb +LP6005442-DNA_A12 SAS_Punjabi_LP6005442-DNA_A12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_A12_wssd.bb +LP6005442-DNA_B01 EAS_Uygur_LP6005442-DNA_B01_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B01_wssd.bb +LP6005442-DNA_B02 AFR_Yoruba_LP6005442-DNA_B02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B02_wssd.bb +LP6005442-DNA_B03 EUR_Bulgarian_LP6005442-DNA_B03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B03_wssd.bb +LP6005442-DNA_B04 EUR_Georgian_LP6005442-DNA_B04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B04_wssd.bb +LP6005442-DNA_B08 EUR_Hungarian_LP6005442-DNA_B08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B08_wssd.bb +LP6005442-DNA_B10 AFR_Esan_LP6005442-DNA_B10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B10_wssd.bb +LP6005442-DNA_B11 EUR_Spanish_LP6005442-DNA_B11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B11_wssd.bb +LP6005442-DNA_B12 SAS_Punjabi_LP6005442-DNA_B12_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_B12_wssd.bb +LP6005442-DNA_C02 EUR_Abkhasian_LP6005442-DNA_C02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_C02_wssd.bb +LP6005442-DNA_C04 EUR_Iranian_LP6005442-DNA_C04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_C04_wssd.bb +LP6005442-DNA_C07 EAS_Ami_LP6005442-DNA_C07_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_C07_wssd.bb +LP6005442-DNA_C10 EUR_Finnish_LP6005442-DNA_C10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_C10_wssd.bb +LP6005442-DNA_C11 EAS_Kinh_LP6005442-DNA_C11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_C11_wssd.bb +LP6005442-DNA_D01 EAS_Xibo_LP6005442-DNA_D01_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D01_wssd.bb +LP6005442-DNA_D02 EUR_Abkhasian_LP6005442-DNA_D02_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D02_wssd.bb +LP6005442-DNA_D03 EUR_Chechen_LP6005442-DNA_D03_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D03_wssd.bb +LP6005442-DNA_D08 EUR_Icelandic_LP6005442-DNA_D08_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D08_wssd.bb +LP6005442-DNA_D09 AFR_Somali_LP6005442-DNA_D09_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D09_wssd.bb +LP6005442-DNA_D10 EUR_Finnish_LP6005442-DNA_D10_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D10_wssd.bb +LP6005442-DNA_D11 EAS_Kinh_LP6005442-DNA_D11_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_D11_wssd.bb +LP6005442-DNA_E04 EUR_Jordanian_LP6005442-DNA_E04_wssd /gbdb/hs1/sgdpCopyNumber/LP6005442-DNA_E04_wssd.bb 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