Try to remove need for PSQL step

[will-moore]

First step (as discussed in IDR meeting today) is to audit the code and check what uses the path and name fields of the Pixels table.

[will-moore]

Trying to see how the Rendering Engine uses Pixels.path and Pixels.name. Seems like most rendering code is in https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/RenderingBean.java but I don't see any reference to path there?

It looks like here we're dealing with Pixels object and not accessing the DB directly?

Searching for JDBC didn't show anything useful.

Also tried search for Duplicate since I remember that this Database access was used in the duplicate logic, but couldn't find anything useful.

@jburel - any pointers?

[will-moore]

Looking at the Stack Trace at #659 (comment)
it looks like this might be a good place to start:

at ome.services.blitz.impl.RenderingEngineI.load_async(RenderingEngineI.java:316)

But I don't see blitz at:
https://github.com/ome/omero-server/tree/master/src/main/java/ome/services

[jburel]

To find the path DuplicateI invokes method in https://github.com/ome/omero-model/blob/master/src/main/java/ome/util/actions/PostgresSqlAction.java#L306
Query is defined in https://github.com/ome/omero-model/blob/master/src/main/resources/ome/util/actions/psql.properties#L5

You need to look into omero-model to understand what is happening

[will-moore]

Thanks.
Looks like that model sql.getPixelsNamePathRepo() is used in getOriginalFilePath() at
https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/OmeroFilePathResolver.java#L53
but I don't see where that is used in omero-server (e.g. for Duplicate or RenderingEngine).

[jburel]

See https://github.com/ome/omero-blitz/blob/master/src/main/java/omero/cmd/graphs/DuplicateI.java#L922

[sbesson]

Possibly relevant to this conversation: while reviewing the histogram server functionality, I was reminded of PixelsService._getPixelBuffer which contains the business logic for selecting the appropriate PixelBuffer (i.e. Bio-Formats vs OMERO Pyramid vs ROMIO) and utilizes the return value of resolver.getOriginalFilePath

[will-moore]

Hmmm, OK so that's 4 repos omero-model, omero-blitz, omero-server, omero-romio that I have to grep to see what uses what. Are there any others?

Searching all for getOriginalFilePath() finds usage in omero-romio PixelsService.java: makePyramid() getBfReader() getPixelBuffer()

getPixelBuffer() is used a lot... will look more closely later...

[will-moore]

getPixelBuffer() is used by (ignoring tests):

• https://github.com/ome/omero-blitz/blob/master/src/main/java/ome/services/roi/PixelData.java
• https://github.com/ome/omero-blitz/blob/master/src/main/java/omero/cmd/fs/FindPyramidsI.java#L222
• https://github.com/ome/omero-server/blob/master/src/main/java/ome/logic/RenderingSettingsImpl.java#L520
• https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/RawPixelsBean.java#L284
• https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/RenderingBean.java#L2205
• https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/ThumbnailBean.java#L354
• https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/projection/ProjectionBean.java#L94 etc

getBFReader() is used by:

• https://github.com/ome/omero-blitz/blob/master/src/main/java/omero/cmd/fs/OriginalMetadataRequestI.java#L137
• https://github.com/ome/omero-blitz/blob/master/src/main/java/omero/cmd/fs/UsedFilesRequestI.java#L195

makePyramid() is used by:

• https://github.com/ome/omero-server/blob/master/src/main/java/ome/services/pixeldata/PixelDataHandler.java#L144

[jburel]

@will-moore I agree that it is not easy to see what's going on following the split

[will-moore]

OK, so lots of places use getOriginalFilePath(), but can we get that path from the Fileset file list instead of the Pixels table?

We need to be sure that the FIRST OriginalFile of the Fileset is the same as that listed in the Pixels table.

Using https://forum.image.sc/t/in-place-import-path-from-image-id-with-omero-database-incoherence-with-originalfile-filesetentry/81509/7

[will-moore]

To test this on a sample of images.. I grabbed an Image ID from each study - using the thumbnails from IDR front page:

let ids = [];
$(".viewer_link").map(function(){ids.push(this.href.split("img_detail/")[1].replace("/", ""))});
JSON.stringify(ids.map(i => parseInt(i)))

[14788721,14788631,14271231,14257890,14239635,14249830,14276397,14000892,14239501,14002649,13994856,13981032,13966432,13966192,13965767,13965888,14231132,13461595,13441324,13457674,13966272,13462232,13425213,13444729,13416991,13422206,12922839,13425427,13417058,12689244,12074276,13457423,11576516,12557110,12539666,12529301,13461816,11512177,10560362,12570400,10340801,10647409,12540310,10502961,11407784,9844391,9846131,9846157,9842150,9822152,9846228,9830833,11550334,9837354,10496304,9836841,10501759,9528933,9798438,12814262,12142871,9840230,8833072,13462847,9036345,8343616,9035363,9822058,12922261,6001240,6001463,9753804,5025551,4495402,5514131,4007817,4995115,9846152,4498386,3509480,4007802,13384350,3428080,3489996,3491629,3414085,4996009,1896580,3414398,3262540,3191907,3125701,3137952,3005373,2858229,3261662,3260524,1885643,7948817,1884913,1911858,1851832,1920105,1755287,2044489,1845698,2865040,1811590,2857890,1921258,1313778,106959,96901,353185,930626,719331,16255,223948,1230459]

Use PSQL to get the name and path for each of those Images from the Pixels table:

select id, path, name from pixels where image in (14788721,14788631,14271231,14257890,14239635,14249830,14276397,14000892,14239501,14002649,13994856,13981032,13966432,13966192,13965767,13965888,14231132,13461595,13441324,13457674,13966272,13462232,13425213,13444729,13416991,13422206,12922839,13425427,13417058,12689244,12074276,13457423,11576516,12557110,12539666,12529301,13461816,11512177,10560362,12570400,10340801,10647409,12540310,10502961,11407784,9844391,9846131,9846157,9842150,9822152,9846228,9830833,11550334,9837354,10496304,9836841,10501759,9528933,9798438,12814262,12142871,9840230,8833072,13462847,9036345,8343616,9035363,9822058,12922261,6001240,6001463,9753804,5025551,4495402,5514131,4007817,4995115,9846152,4498386,3509480,4007802,13384350,3428080,3489996,3491629,3414085,4996009,1896580,3414398,3262540,3191907,3125701,3137952,3005373,2858229,3261662,3260524,1885643,7948817,1884913,1911858,1851832,1920105,1755287,2044489,1845698,2865040,1811590,2857890,1921258,1313778,106959,96901,353185,930626,719331,16255,223948,1230459);

psql output

``` id | path | name ----------+--------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------------------- 16255 | demo_2/2015-09/07/11-28-34.406 | experiment_descriptor.xml 96901 | demo_2/2015-09/16/11-37-28.997 | 009007000.flex 106959 | demo_2/2015-09/22/13-44-54.603 | Act1_Plate10-SP-A8.HTD 223948 | demo_2/2015-09/23/12-56-08.713 | experiment_descriptor.xml 353185 | demo_2/2015-09/24/14-38-23.240 | plate 11001.HTD 719331 | demo_2/2015-10/01/11-45-16.436/homes/jamoore/rad52/idr0004-thorpe-rad52/screens | p120.screen 930626 | demo_2/2015-10/02/11-54-37.257 | 2011-08-29-plateb-004.HTD 1230459 | demo_2/2015-11/23/16-25-19.109/Meas_01(2012-07-31_18-32-21) | 001001001.flex 1313778 | demo_2/2015-11/26/07-22-16.896 | experiment_descriptor.xml 1755287 | demo_2/2016-05/15/02-35-02.228 | 2011-11-17 X-Man LOPAC_X12_LP_S02_1.xdce 1811590 | demo_2/Blitz-0-Ice.ThreadPool.Server-9/2023-05/11/10-30-57.116/HT01.ome.zarr/OME | METADATA.ome.xml 1845698 | demo_2/2016-05/17/01-31-52.963/idrdata/idr-metadata/idr0015-UNKNOWN-taraoceans/screenA/patterns | TARA_HCS1_H5_G100001988_G100001989--2013_09_23_19_42_50_chamber--U00--V01.screen 1851832 | demo_2/2016-05/17/12-18-41.461/Raw images - OME tif files by plate/22_lines_HC_EGF_200145913 | MeasurementIndex.ColumbusIDX.xml 1884913 | demo_2/2016-05/18/08-48-03.837 | Cep152_gtub_006_SIR_PRJ.dv 1885643 | demo_2/2016-05/18/12-38-31.236 | SUM_trans_norm.tif 1896580 | demo_2/2016-05/19/00-15-38.492/idrdata/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens | 20585.screen 1911858 | demo_2/2016-05/19/20-47-07.067/Alexis 040413 hMAP screen[2056]/200972432 NS[2668] | MeasurementIndex.ColumbusIDX.xml 1920105 | demo_2/2016-05/20/16-46-18.092 | Bazla-14-100-gi - 2015-06-20 00.24.01.ndpi 1921258 | demo_2/Blitz-0-Ice.ThreadPool.Server-3/2023-05/18/20-35-15.516/1-23.ome.zarr/OME | METADATA.ome.xml 2044489 | demo_2/2016-06/15/22-36-23.585/metadata/idr0016-wawer-bioactivecompoundprofiling/screens | 24278.screen 2857890 | demo_2/2016-07/28/21-44-02.006/metadata/idr0011-thorpe-Dad4/screens | TS-Stinger-Target-1&2.screen 2858229 | demo_2/2016-07/29/13-20-08.915 | v_upper_t_lower_ALX.dv 2865040 | demo_2/2016-09/21/07-41-29.038/metadata/idr0013-neumann-mitocheck/screens | LTValidMitosisSon384Plate03_02--ex2009_03_11--sp2009_01_27--tt17--c6.screen 3005373 | demo_2/2016-10/02/08-13-41.685/MDA-MB-231_GEFGAP_ONTARGETPlus/MDA-MB-231_GEFGAP_ONTARGETPlus_1A | MeasurementIndex.ColumbusIDX.xml 3125701 | demo_2/2017-01/17/10-01-58.931 | 1.tif 3137952 | demo_2/2017-03/03/23-39-52.110/20170110-original/200972727[5177]_kinome_YAP_CD44 | MeasurementIndex.ColumbusIDX.xml 3191907 | demo_2/2017-03/06/14-24-32.180/data/idr-metadata/idr0033-rohban-pathways/screens | 41744.screen 3260524 | demo_2/2017-03/13/15-19-51.590/data/idr-metadata/idr0025-stadler-proteinatlas/screens | 10x images plate 1.screen 3261662 | demo_2/2017-04/12/14-50-01.387/tmp/idr-metadata/idr0026-weigelin-immunotherapy/patterns | 3.55.6-3.140922_15-36-34.01.pattern 3262540 | demo_2/2017-05/03/16-23-06.157/Images | Index.idx.xml 3414085 | demo_2/2017-11/25/21-35-58.834 | Time-PNA-rh-vital-test.czi 3414398 | demo_2/2018-01/24/11-03-15.125/data/idr-metadata/idr0035-caie-drugresponse/screens | Week10_40115.screen 3428080 | demo_2/2018-03/29/09-27-23.478 | 33380_0_fal_24_0.png 3489996 | demo_2/2018-04/04/18-04-03.255 | TR1_2_W0001_P0009_T0032.tif 3491629 | demo_2/2018-04/05/20-50-21.990 | img_000000001_07-YFPtriple_000.tif 3509480 | demo_2/2018-08/23/10-13-22.623 | Embryo8.pattern 4007802 | demo_2/Blitz-0-Ice.ThreadPool.Server-19/2018-11/26/09-57-43.807/Mmu_E1_CAGTAG1.TM000036_timeFused_blending | SPM00_TM000036_CM00_CM01_CHN01.fusedStack_yzProjection.corrected.shifted.klb 4007817 | demo_2/Blitz-0-Ice.ThreadPool.Server-24/2018-11/26/10-39-10.551/patterns | 180712_H2B_22ss_Courtney1_20180712-163837_p00_c00_preview.pattern 4495402 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2019-01/07/11-41-55.076 | fig1.tif 4498386 | demo_2/Blitz-0-Ice.ThreadPool.Server-9/2019-01/15/17-17-44.268 | Exp2_rep2_15min_im2.companion.ome 4995115 | demo_2/Blitz-0-Ice.ThreadPool.Server-1/2019-02/02/04-12-08.857 | ExperimentB_No07_Noc_10_10min__019.czi 4996009 | demo_2/Blitz-0-Ice.ThreadPool.Server-1/2019-02/22/16-14-26.593/20140424_HipSci + BJ 3000c_well_OC__2014-04-24T17_01_22-Measurement1/Images | Index.idx.xml 5025551 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2023-05/18/09-50-49.857/Tonsil 1.ome.zarr/OME | METADATA.ome.xml 5514131 | demo_2/Blitz-0-Ice.ThreadPool.Server-35/2019-04/07/16-52-18.169 | c0011_r0001_ana_early.companion.ome 6001240 | demo_2/Blitz-0-Ice.ThreadPool.Server-23/2019-06/07/11-47-40.029 | B1_C1.tif 6001463 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2019-06/25/08-24-31.647 | BSF012983_1_1.xdce 7948817 | demo_2/Blitz-0-Ice.ThreadPool.Server-28/2019-07/31/06-41-49.838 | Experiment.exp 8343616 | demo_2/Blitz-0-Ice.ThreadPool.Server-18/2019-09/17/08-39-08.915 | ExpD_chicken_embryo_MIP.ome.tif 8833072 | demo_2/Blitz-0-Ice.ThreadPool.Server-24/2019-10/15/13-47-39.435/1315001__2014-01-25T18_26_59-Measurement1/Images | Index.idx.xml 9035363 | demo_2/Blitz-0-Ice.ThreadPool.Server-10/2019-11/25/14-00-58.842 | subpool-6_run-2_EXP-18-BQ3521_round-01.companion.ome 9036345 | demo_2/Blitz-0-Ice.ThreadPool.Server-16/2019-12/09/11-11-43.847 | 1B_MAX_010618_Hsp104Htb1_Meiosis_01_47_zproj_R3D_D3D.tif 9528933 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2020-01/14/09-00-54.866 | MBLipOverviewBee1.companion.ome 9753804 | demo_2/Blitz-0-Ice.ThreadPool.Server-3/2020-01/31/10-14-49.900/Plate1_screen3/150115_103503-V[2405] | MeasurementIndex.ColumbusIDX.xml 9798438 | demo_2/Blitz-0-Ice.ThreadPool.Server-21/2020-02/10/13-31-20.181 | breastCancer17.ome.tiff 9822058 | demo_2/Blitz-0-Ice.ThreadPool.Server-1/2020-04/23/14-58-14.924/metadata/idr0064-goglia-erkdynamics/screens | 3.2.screen 9822152 | demo_2/Blitz-0-Ice.ThreadPool.Server-2/2020-04/27/11-24-15.526 | 12448_G1HR_Mesh003.tif 9830833 | demo_2/Blitz-0-Ice.ThreadPool.Server-0/2020-05/06/00-07-22.768 | Antivir_screen_Adv_BSF018292_1.xdce 9836841 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2020-06/16/09-53-32.715 | 2018-12-18 ASY H2B bud 05 3D 8 angles_Maximum intensity projection.czi 9837354 | demo_2/Blitz-0-Ice.ThreadPool.Server-10/2020-06/22/13-59-43.244 | EE5CF455D9.companion.ome 9840230 | demo_2/Blitz-0-Ice.ThreadPool.Server-9/2020-06/23/14-15-34.755 | N703_099_2.jpg 9842150 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2020-07/10/11-12-03.163 | 2017-07-24-No_primary-01_10_R3D.dv 9844391 | demo_2/Blitz-0-Ice.ThreadPool.Server-15/2020-07/16/13-01-55.968 | exp_A01_G001_0008.oir 9846131 | demo_2/Blitz-0-Ice.ThreadPool.Server-18/2020-07/17/10-15-41.810 | Figure_S3C_FIB-SEM_HeLa_G1_20x20x20nm_xy.tif 9846152 | demo_2/Blitz-0-Ice.ThreadPool.Server-14/2020-08/04/12-20-13.931 | WB.xml 9846157 | demo_2/Blitz-0-Ice.ThreadPool.Server-15/2020-08/06/15-40-56.177 | Brain_two_channel_CMDiI_HCSCellMask_pxl_xy_4.47_pxl_z_2.58.tif 9846228 | demo_2/Blitz-0-Ice.ThreadPool.Server-12/2020-08/18/16-04-59.361 | S14_HandE.ndpi 10340801 | demo_2/Blitz-0-Ice.ThreadPool.Server-4/2020-09/01/11-35-48.652 | Plate1.companion.ome 10496304 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2020-09/05/15-40-12.840/BR1/TSA2-RT | Index.idx.xml 10501759 | demo_2/Blitz-0-Ice.ThreadPool.Server-3/2020-09/17/15-30-38.111 | MB0020_1_88_fullstack.tiff 10502961 | demo_2/Blitz-0-Ice.ThreadPool.Server-2/2020-09/18/13-08-16.173 | AC16_T18d24h37d2h_Rep1_PoorProbeChan1_Cry2Chan2_DAPIChan3_13.dv 10560362 | demo_2/Blitz-0-Ice.ThreadPool.Server-5/2020-09/30/17-16-21.544/ESP0025713[6258]/2020-03-24T123102+0100[6571] | MeasurementIndex.ColumbusIDX.xml 10647409 | demo_2/Blitz-0-Ice.ThreadPool.Server-14/2020-10/02/09-01-15.252 | 20151204_switch6h_1_MMStack_Pos0_metadata.txt 11407784 | demo_2/Blitz-0-Ice.ThreadPool.Server-7/2020-10/23/03-19-34.107/1013608208 | 1013608208.wpi 11512177 | demo_2/Blitz-0-Ice.ThreadPool.Server-7/2020-11/12/14-02-05.854 | no.nd2 11550334 | demo_2/Blitz-0-Ice.ThreadPool.Server-13/2020-12/03/12-06-29.564/Images | Index.idx.xml 11576516 | demo_2/Blitz-0-Ice.ThreadPool.Server-14/2020-12/08/15-30-31.102 | Sample2.pattern 12074276 | demo_2/Blitz-0-Ice.ThreadPool.Server-4/2021-01/11/11-41-59.090 | R3-C1--C2-100mM2DG_400ug_Chol_JRFL_32bit-NEW.ome.tif 12142871 | demo_2/Blitz-0-Ice.ThreadPool.Server-3/2021-01/14/20-19-49.463 | 10X_c6-SBS-6_A2_Tile-471.sbs.companion.ome 12529301 | demo_2/Blitz-0-Ice.ThreadPool.Server-13/2021-02/05/20-30-14.424/ExperimentA/Plate1 | Index.idx.xml 12539666 | demo_2/Blitz-0-Ice.ThreadPool.Server-15/2021-02/08/09-49-23.053 | S008a.ndpi 12540310 | demo_2/Blitz-0-Ice.ThreadPool.Server-5/2021-02/18/20-50-17.861/metadata/idr0090-ashdown-malaria/screens | 190129.screen 12557110 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2021-02/23/17-07-39.677 | TP_Ch0_Ill0_Ang1,2,3,4,5.tif.companion.ome 12570400 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2021-03/06/15-00-54.048/005 | 005.wpi 12689244 | demo_2/Blitz-0-Ice.ThreadPool.Server-13/2021-03/09/16-03-40.697 | Mosaic_Image.companion.ome 12814262 | demo_2/Blitz-0-Ice.ThreadPool.Server-4/2021-04/23/23-59-47.230 | 003011000.flex 12922261 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2021-04/27/10-30-20.237 | URA3SP2_t2.tif 12922839 | demo_2/Blitz-0-Ice.ThreadPool.Server-10/2021-05/26/02-24-03.410 | 150626_m528_UT8.nd2 13384350 | demo_2/Blitz-0-Ice.ThreadPool.Server-20/2021-06/11/07-33-45.511 | 165383_A_3_2.tif 13416991 | demo_2/Blitz-0-Ice.ThreadPool.Server-10/2021-06/22/12-06-14.288 | 2021-01-11_plate22021-01-11_plate2_WellA4.ome.tiff 13417058 | demo_2/Blitz-0-Ice.ThreadPool.Server-1/2021-06/23/12-35-28.539 | Composite.tif 13422206 | demo_2/Blitz-0-Ice.ThreadPool.Server-4/2021-07/20/00-22-58.569 | 20200201_Pulse_Chase_turnover_on_chromatin_CIZ1KO_NPC_220min_01_FUS.dv 13425213 | demo_2/Blitz-0-Ice.ThreadPool.Server-7/2021-07/20/10-34-45.738 | Image5D_bf3092_SPOT1.tif 13425427 | demo_2/Blitz-0-Ice.ThreadPool.Server-7/2021-08/10/14-09-15.167 | 02_638i100_640i150_405i50_x20_1_MMStack2.ome.tif 13441324 | demo_2/Blitz-0-Ice.ThreadPool.Server-2/2021-08/26/14-48-02.788 | SkeT Plut.tif 13444729 | demo_2/Blitz-0-Ice.ThreadPool.Server-10/2021-08/31/10-08-15.217 | plate7.companion.ome 13457423 | demo_2/Blitz-0-Ice.ThreadPool.Server-12/2021-09/06/10-56-35.082 | cell001.pattern 13457674 | demo_2/Blitz-0-Ice.ThreadPool.Server-11/2021-09/13/14-22-24.677 | 6229-246.ome.tiff 13461595 | demo_2/Blitz-0-Ice.ThreadPool.Server-3/2021-11/03/19-36-45.530 | fkh_sample1_Raw_Images.tif 13461816 | demo_2/Blitz-0-Ice.ThreadPool.Server-38/2021-11/09/11-54-24.914 | 319.ome.tiff 13462232 | demo_2/Blitz-0-Ice.ThreadPool.Server-12/2021-11/29/11-21-28.745 | 12204,1,Head,CS23,74_CHRNB2.ome.tiff 13462847 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2021-12/05/20-03-24.490 | image.ome.tiff 13965767 | demo_2/Blitz-0-Ice.ThreadPool.Server-3/2022-01/10/17-58-40.152 | E14.lif 13965888 | demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-02/15/17-24-43.482 | Dataset1.companion.ome 13966192 | demo_2/Blitz-0-Ice.ThreadPool.Server-9/2022-02/19/10-20-43.639 | CI1564_exponential_TL.ome.tiff 13966272 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2022-04/19/14-30-13.374 | 160701-Nup107-cell-2-t6.tif 13966432 | demo_2/Blitz-0-Ice.ThreadPool.Server-6/2022-04/28/08-48-18.913 | Antivir_screen_IAV_BSF019243_1.xdce 13981032 | demo_2/Blitz-0-Ice.ThreadPool.Server-4/2022-04/29/10-01-28.225 | Antivir_screen_HRV_BSF019072_1.xdce 13994856 | demo_2/Blitz-0-Ice.ThreadPool.Server-16/2022-04/29/15-44-08.495 | 190725-3-36-HSV-1A.HTD 14000892 | demo_2/Blitz-0-Ice.ThreadPool.Server-1/2022-05/02/11-29-38.196 | Eran Hodis 2020-09-14-012.svs 14002649 | demo_2/Blitz-0-Ice.ThreadPool.Server-9/2022-06/23/08-03-31.042 | BR00109990.companion.ome 14231132 | demo_2/Blitz-0-Ice.ThreadPool.Server-20/2022-07/15/08-13-44.234 | plate.companion.ome 14239501 | demo_2/Blitz-0-Ice.ThreadPool.Server-13/2022-08/11/22-14-28.679 | scapania_ornithopodioides_stature_ventral_side.ome.tiff 14239635 | demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-09/15/09-35-20.511 | Sokol_04.ome.tiff 14249830 | demo_2/Blitz-0-Ice.ThreadPool.Server-19/2022-10/19/09-32-55.401 | 003012001.flex 14257890 | demo_2/Blitz-0-Ice.ThreadPool.Server-7/2022-12/02/18-40-27.618 | F_46.ome.tiff 14271231 | demo_2/Blitz-0-Ice.ThreadPool.Server-15/2022-12/15/22-05-13.977 | 003012001.flex 14276397 | demo_2/Blitz-0-Ice.ThreadPool.Server-18/2022-12/18/20-23-35.659 | IMG_0506-0555 Riccia sorocarpa stature (Laowa 5.0x).ome.tiff ```

Then I used a python script test_getOriginalFile_from_fileset.py based on the query above to get the first original file associated with each Image and printed out any mismatches (after joining path and name). The 1st of each mismatch is from the Fileset.OriginalFile and the 2nd is from the Pixels table:

image_id 1230459
demo_2/2015-11/23/16-25-19.109/Meas_05(2012-07-31_23-29-17)/001001001.flex
demo_2/2015-11/23/16-25-19.109/Meas_01(2012-07-31_18-32-21)/001001001.flex
image_id 1811590
demo_2/2016-05/16/14-53-28.229/uod/idr/filesets/idr0012-fuchs-cellmorph/downloaded/primary/source/www.ebi.ac.uk/huber-srv/cellmorph/source/HT01/HT01F008/HT01F008_A1.tif
demo_2/Blitz-0-Ice.ThreadPool.Server-9/2023-05/11/10-30-57.116/HT01.ome.zarr/OME/METADATA.ome.xml
image_id 1845698
demo_2/2016-05/17/01-31-52.963/uod/idr/filesets/idr0015-UNKNOWN-taraoceans/20150918-tara/RAW_DATA/TARA_HCS1_H5_G100001988_G100001989--2013_09_23_19_42_50/slide--S00/chamber--U00--V01/field--X17--Y18/image--L00--S00--U00--V01--J08--E00--O00--X17--Y18--T00--Z00--C00.ome.tif
demo_2/2016-05/17/01-31-52.963/idrdata/idr-metadata/idr0015-UNKNOWN-taraoceans/screenA/patterns/TARA_HCS1_H5_G100001988_G100001989--2013_09_23_19_42_50_chamber--U00--V01.screen
image_id 1896580
demo_2/2016-05/19/00-15-38.492/uod/idr/incoming/idr0016-wawer-bioactivecompoundprofiling/2016-01-19-screens-bbbc022/20585-ERSytoBleed/IXMtest_A01_s1_w3FD54227A-6BE4-460B-8E2C-54B8709F6E33.tif
demo_2/2016-05/19/00-15-38.492/idrdata/idr-metadata/idr0016-wawer-bioactivecompoundprofiling/screens/20585.screen
image_id 1911858
demo_2/2016-05/19/20-47-07.067/Alexis 040413 hMAP screen[2056]/200972432 NS[2668]/2013-04-04T234449Z[7406]/ImageIndex.ColumbusIDX.csv
demo_2/2016-05/19/20-47-07.067/Alexis 040413 hMAP screen[2056]/200972432 NS[2668]/MeasurementIndex.ColumbusIDX.xml
image_id 1921258
demo_2/2016-05/21/00-22-55.102/idrdata/idr-metadata/idr0010-doil-dnadamage/screenA/plates/1-23.pattern
demo_2/Blitz-0-Ice.ThreadPool.Server-3/2023-05/18/20-35-15.516/1-23.ome.zarr/OME/METADATA.ome.xml
image_id 2044489
demo_2/2016-06/15/22-36-23.585/incoming/idr0016-wawer-bioactivecompoundprofiling/2016-02-19-screens-cellimagelibrary/24278-ERSyto/cdp2bioactives_a01_s1_w2edcec6dc-b1e3-4ffc-80da-9b049a89447b.tif
demo_2/2016-06/15/22-36-23.585/metadata/idr0016-wawer-bioactivecompoundprofiling/screens/24278.screen
image_id 2865040
demo_2/2016-09/21/07-41-29.038/filesets/idr0013-neumann-mitocheck/20150916-mitocheck-analysis/analysis/mitocheck/LTValidMitosisSon384Plate03_02--ex2009_03_11--sp2009_01_27--tt17--c6/hdf5/00001_01.ch5
demo_2/2016-09/21/07-41-29.038/metadata/idr0013-neumann-mitocheck/screens/LTValidMitosisSon384Plate03_02--ex2009_03_11--sp2009_01_27--tt17--c6.screen
image_id 3137952
demo_2/2017-03/03/23-39-52.110/20170110-original/200972727[5177]_kinome_YAP_CD44/2014-09-21T053223Z[18861]/ImageIndex.ColumbusIDX.csv
demo_2/2017-03/03/23-39-52.110/20170110-original/200972727[5177]_kinome_YAP_CD44/MeasurementIndex.ColumbusIDX.xml
image_id 3191907
demo_2/2017-03/06/14-24-32.180/uod/idr/filesets/idr0033-rohban-pathways/20170214-original/images/41744/taoe005-u2os-72h-cp-a-au00044859_a01_s1_w1506fb051-c2ad-45db-8a52-674278937a31.tif
demo_2/2017-03/06/14-24-32.180/data/idr-metadata/idr0033-rohban-pathways/screens/41744.screen
image_id 3260524
demo_2/2017-03/13/15-19-51.590/uod/idr/filesets/idr0025-stadler-proteinatlas/20160525-rawdata/10x images plate 1/plate 1 A7B7 ab 7 c10orf58/Sequence/Loop_ 0/A 0_L 0_S 0_U 5_V 0_X 0_Y 0_Job(Seq.Scan) 1 01 01_001_z0_ch00.tif
demo_2/2017-03/13/15-19-51.590/data/idr-metadata/idr0025-stadler-proteinatlas/screens/10x images plate 1.screen
image_id 4007802
demo_2/Blitz-0-Ice.ThreadPool.Server-19/2018-11/26/09-57-43.807/Mmu_E1_CAGTAG1.TM000098_timeFused_blending/SPM00_TM000098_CM00_CM01_CHN00.fusedStack.corrected.shifted.klb
demo_2/Blitz-0-Ice.ThreadPool.Server-19/2018-11/26/09-57-43.807/Mmu_E1_CAGTAG1.TM000036_timeFused_blending/SPM00_TM000036_CM00_CM01_CHN01.fusedStack_yzProjection.corrected.shifted.klb
image_id 4007817
demo_2/Blitz-0-Ice.ThreadPool.Server-24/2018-11/26/10-39-10.551/20181025-ftp/Dataset_3/Unprocessed Image Files/180712_H2B_22ss_Courtney1_20180712-163837_p00_c00_t0000_preview.ome.tiff
demo_2/Blitz-0-Ice.ThreadPool.Server-24/2018-11/26/10-39-10.551/patterns/180712_H2B_22ss_Courtney1_20180712-163837_p00_c00_preview.pattern
image_id 4498386
demo_2/Blitz-0-Ice.ThreadPool.Server-9/2019-01/15/17-17-44.268/#2_Analyzed_images/M_nuclei_Exp2_rep2_15min_im2_nuclei3D.tiff
demo_2/Blitz-0-Ice.ThreadPool.Server-9/2019-01/15/17-17-44.268/Exp2_rep2_15min_im2.companion.ome
image_id 4996009
demo_2/Blitz-0-Ice.ThreadPool.Server-1/2019-02/22/16-14-26.593/20140424_HipSci + BJ 3000c_well_OC__2014-04-24T17_01_22-Measurement1/Evaluation2/HipSci_Pipeline_2014-07-31-current.aas
demo_2/Blitz-0-Ice.ThreadPool.Server-1/2019-02/22/16-14-26.593/20140424_HipSci + BJ 3000c_well_OC__2014-04-24T17_01_22-Measurement1/Images/Index.idx.xml
image_id 5025551
demo_2/Blitz-0-Ice.ThreadPool.Server-5/2019-03/15/15-27-40.023/Tonsil 1/Tonsil 1_C00.png
demo_2/Blitz-0-Ice.ThreadPool.Server-6/2023-05/18/09-50-49.857/Tonsil 1.ome.zarr/OME/METADATA.ome.xml
image_id 5514131
demo_2/Blitz-0-Ice.ThreadPool.Server-35/2019-04/07/16-52-18.169/c0011_r0001_ana_early/c0011_r0001_Chr_20170831_Samples20170818_NCAPD3-mEGFP_A_ana-early3_region1_Hoechst.tif
demo_2/Blitz-0-Ice.ThreadPool.Server-35/2019-04/07/16-52-18.169/c0011_r0001_ana_early.companion.ome
image_id 7948817
demo_2/Blitz-0-Ice.ThreadPool.Server-28/2019-07/31/06-41-49.838/Well H02/Transmitted Light - n000000.tif
demo_2/Blitz-0-Ice.ThreadPool.Server-28/2019-07/31/06-41-49.838/Experiment.exp
image_id 9035363
demo_2/Blitz-0-Ice.ThreadPool.Server-10/2019-11/25/14-00-58.842/Pos133/4_fam_flour/01.tiff
demo_2/Blitz-0-Ice.ThreadPool.Server-10/2019-11/25/14-00-58.842/subpool-6_run-2_EXP-18-BQ3521_round-01.companion.ome
image_id 9822058
demo_2/Blitz-0-Ice.ThreadPool.Server-1/2020-04/23/14-58-14.924/filesets/idr0064-goglia-erkdynamics/20190630-ftp/Plate 3.2/plate_3-2_405_01.nd2.tif_merged.tif
demo_2/Blitz-0-Ice.ThreadPool.Server-1/2020-04/23/14-58-14.924/metadata/idr0064-goglia-erkdynamics/screens/3.2.screen
image_id 10496304
demo_2/Blitz-0-Ice.ThreadPool.Server-6/2020-09/05/15-40-12.840/BR1/TSA2-37/Index.idx.xml
demo_2/Blitz-0-Ice.ThreadPool.Server-6/2020-09/05/15-40-12.840/BR1/TSA2-RT/Index.idx.xml
image_id 12529301
demo_2/Blitz-0-Ice.ThreadPool.Server-13/2021-02/05/20-30-14.424/ExperimentA/Plate8/Index.idx.xml
demo_2/Blitz-0-Ice.ThreadPool.Server-13/2021-02/05/20-30-14.424/ExperimentA/Plate1/Index.idx.xml

So it looks like there's quite a few where using the first OriginalFile from the Fileset wouldn't give the same path/name as you'd get from querying the Pixels table.