Bug: broken download urls

[will-moore]

From #67

OK, let's document all the GitHub and other studies where:

• this new /image/ID/download_urls/ doesn't work
• Of these which are "zarr" images (we care less about these as the iviewer works - no placeholder page)

Failing studies

• idr0170 (zarr) data/idr-metadata/idr0170-rose-mibitof/experimentA/../metadata/RPM-TMA-1_ROI01_multichannel.ome.xml Images are named like RPM-TMA-1_ROI01_multichannel.zarr which needs to download https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/961/S-BIAD1961/Files/experimentA/RPM-TMA/RPM-TMA-1_ROI01_multichannel.zarr.zip - Download url is https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/961/S-BIAD1961/Files/experimentA/RPM-TMA/ + image-name + .zip

• idr0168 (zarr) Image name: A375_6_ATP13A5_Z-stack_HF_01_2024-03-06_YunHao_23.31.23.zarr - Download url https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/891/S-BIAD1891/Files/A375_6_ATP13A5_Z-stack_HF_01_2024-03-06_YunHao_23.31.23.zarr.tgz is https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/891/S-BIAD1891/Files/ + name + .tgz

• idr0163 S-BIAD1288 Download url is https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/288/S-BIAD1288/Files/TONIC/image_data/samples/ + name + .zip

• idr0106 (github) - Single image. LOTs of files in fileset. companion on GitHub (working). Download tiffs from https://ftp.ebi.ac.uk/pub/databases/IDR/idr0106-kubota-lunglightsheet/20210226/Mosaic%20Image_Z%5b00001%5d_L%5b1%5d.ome.tiff - replace data/idr-metadata/idr0106-kubota-lunglightsheet/experimentA/companions/ with https://ftp.ebi.ac.uk/pub/databases/IDR/idr0106-kubota-lunglightsheet/20210226/. e.g.

  • data/idr-metadata/idr0106-kubota-lunglightsheet/experimentA/companions/Mosaic_Image.companion.ome (github)
  • data/idr-metadata/idr0106-kubota-lunglightsheet/experimentA/companions/Mosaic Image_Z[00001]_L[1].ome.tiff

• idr0096: Need to replace # in url e.g. https://ftp.ebi.ac.uk/pub/databases/IDR/idr0096-tratwal-marrowquant/20210609-ftp-ome-tiffs/m4%20pelvic%20(20x%20#2).ome.tiff

• idr0090 (zarr - mkngff) Download multiple (10) zarr.zips per Plate: https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/882/S-BIAD882/Files/idr0090/ - e.g. https://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/882/S-BIAD882/Files/idr0090/190129.ome.zarr.zip.011 - https://idr-testing.openmicroscopy.org/image/12539701/download_urls/ gives ALL zarr files (except chunks)

• idr0079 (GitHub) companion.ome is OK USE .raw link! uod/idr/metadata/idr0079-hartmann-lateralline/companions/experimentA/056F63395C/056F63395C_8bit_lynEGFP.tif to https://ftp.ebi.ac.uk/pub/databases/IDR/idr0079-hartmann-lateralline/20200220-ftp/experimentA/056F63395C/056F63395C_8bit_lynEGFP.tif Replace uod/idr/metadata/idr0079-hartmann-lateralline/companions/ with https://ftp.ebi.ac.uk/pub/databases/IDR/idr0079-hartmann-lateralline/20200220-ftp/

• id0075 - companion OK. tif uod/idr/metadata/idr0075-cabirol-honeybee/experimentA/companions/MBLipOverviewBee1.tif https://ftp.ebi.ac.uk/pub/databases/IDR/idr0075-cabirol-honeybee/20191129-ftp/Raw%20Images/MBLipOverviewBee1.tif replace uod/idr/metadata/idr0075-cabirol-honeybee/experimentA/companions/ with https://ftp.ebi.ac.uk/pub/databases/IDR/idr0075-cabirol-honeybee/20191129-ftp/Raw%20Images/

• idr0071 - https://ftp.ebi.ac.uk/pub/databases/IDR/idr0071-feldman-crisprko/20201027-companions/companions/experimentA/process/10X_A1_Tile-102.aligned.tif is 404. No tifs in https://ftp.ebi.ac.uk/pub/databases/IDR/idr0071-feldman-crisprko/20201027-companions/companions/experimentA/process/ ???

• idr0065 (GitHub) uod/idr/metadata/idr0065-camsund-crispri/experimentA/companions/subpool-1_run-1_EXP-19-BQ3550/pheno/Pos101/phase/img_000000000.tiff - Too tricky to work this out!! https://ftp.ebi.ac.uk/pub/databases/IDR/idr0065-camsund-crispri/ has 3 ftp uploads (not in client_paths)

• idr0099 data/idr-metadata/idr0099-jain-beetlelightsheet/experimentA/20210208-patterns/9-3-15_Histone-eGFP/TP_T0_Chgreen_Ill0_Ang0,1,2.tif to https://ftp.ebi.ac.uk/pub/databases/IDR/idr0099-jain-beetlelightsheet/20201001-ftp/Akanksha_Jain_9-3-15_Histone-eGFP/TP0_Chgreen_Ill0_Ang0,1,2.tif BUT also data/idr-metadata/idr0099-jain-beetlelightsheet/experimentA/20210128-companions/22-06-16_Tc-Squash-eGFP/TP0_Ch0_Ill0_Ang1,2,3,4,5.tif to https://ftp.ebi.ac.uk/pub/databases/IDR/idr0099-jain-beetlelightsheet/20210128-ftp/TP0_Ch0_Ill0_Ang1,2,3,4,5.tif - NO simple replace, - same image: data/idr-metadata/idr0099-jain-beetlelightsheet/experimentA/20210128-companions/22-06-16_Tc-Squash-eGFP/TP212_Ch0_Ill0_Ang1,2,3,4,5.tif to https://ftp.ebi.ac.uk/pub/databases/IDR/idr0099-jain-beetlelightsheet/20201001-ftp/Akanksha_Jain_22-06-16_Tc-Squash-eGFP/TP212_Ch0_Ill0_Ang1,2,3,4,5.tif NB: https://ftp.ebi.ac.uk/pub/databases/IDR/idr0099-jain-beetlelightsheet/20210128-ftp/ only has 11 tiffs, all the rest are under https://ftp.ebi.ac.uk/pub/databases/IDR/idr0099-jain-beetlelightsheet/20201001-ftp/

[will-moore]

See IDR/idr.openmicroscopy.org#225 where some github studies are fixed