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Curated metadata for all studies published in the Image Data Resource
https://idr.openmicroscopy.org
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idr0009 ScanR missing Wells #684

Open will-moore opened 8 months ago

will-moore commented 8 months ago

Currently on idr-next (prod120) idr0009 Plates are not handling missing Wells correctly.

Seb: “The problem is that this data was originally loaded with a version of the ScanR reader that represents missing wells as black images while the default behavior in Bio-Formats is to represent these as sparse plates. When this was backported to OME Bio-Formats, an option was introduced to support both behaviors - see https://bio-formats.readthedocs.io/en/latest/formats/options.html I think the action is to update all plates in this study to set scanr.skip_missing_wells to false , delete & regenerate the memo files and retest”

will-moore commented 8 months ago

Tested this (originally posted at https://github.com/IDR/idr-metadata/issues/675#issuecomment-1881406444)...

For idr0009 - need to add scanr.skip_missing_wells=false to a .bfoptions file for every Plate (964 plates)! E.g. ?show=well-607352 plate has missing Wells. Trying to view any image after missing Wells shows wrong Image or error.

Fileset template prefixes - test with just a couple from that Plate and the next

http://localhost:1080/webclient/?show=plate-2703 http://localhost:1080/webclient/?show=plate-2705

bash-4.2$ cat idr0009_filesetprefix.csv
demo_2/2015-11/26/07-41-09.642
demo_2/2015-11/26/07-41-14.425

For each, create experiment_descriptor.xml.bfoptions

 for f in $(cat idr0009_filesetprefix.csv); do echo "scanr.skip_missing_wells=false" > "/data/OMERO/ManagedRepository/$f/experiment_descriptor.xml.bfoptions"; done

This has created .bfoptions file... for http://localhost:1080/webclient/?show=plate-2705

bash-4.2$ ls -alh /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-14.425
total 112K
drwxrwxr-x.  3 omero-server omero-server  153 Jan  8 15:43 .
drwxrwxr-x. 72 omero-server omero-server 8.0K Nov 26  2015 ..
lrwxrwxrwx.  1 omero-server omero-server   97 Nov 26  2015 AcquisitionLog.dat -> /idr/filesets/idr0009-simpson-secretion/20150507-VSVG/VSVG/0305-10--2007-04-10/AcquisitionLog.dat
drwxrwxr-x.  2 omero-server omero-server  72K Nov 26  2015 data
lrwxrwxrwx.  1 omero-server omero-server  104 Nov 26  2015 experiment_descriptor.dat -> /idr/filesets/idr0009-simpson-secretion/20150507-VSVG/VSVG/0305-10--2007-04-10/experiment_descriptor.dat
lrwxrwxrwx.  1 omero-server omero-server  104 Nov 26  2015 experiment_descriptor.xml -> /idr/filesets/idr0009-simpson-secretion/20150507-VSVG/VSVG/0305-10--2007-04-10/experiment_descriptor.xml
-rw-r--r--.  1 omero-server omero-server   31 Jan  8 15:43 experiment_descriptor.xml.bfoptions

The bfmemo exists for some Plates, e.g. first Plate of idr0009 on idr-testing:

ls -alh /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-22-16.896
total 448K
drwxrwxr-x. 2 omero-server omero-server   47 Nov 30 17:36 .
drwxrwxr-x. 5 omero-server omero-server   66 Jan  8 15:58 ..
-rw-rw-r--. 1 omero-server omero-server 448K Nov 30 17:36 .experiment_descriptor.xml.bfmemo

and for Plate above http://localhost:1080/webclient/?show=plate-2705 with some missing Wells

bash-4.2$ ls -alh /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-14.425
total 444K
drwxrwxr-x. 2 omero-server omero-server   47 Jan  8 15:37 .
drwxrwxr-x. 5 omero-server omero-server   66 Jan  8 15:58 ..
-rw-rw-r--. 1 omero-server omero-server 443K Jan  8 15:37 .experiment_descriptor.xml.bfmemo

but not for other plates with missing Wells - e.g. first plate above

bash-4.2$ ls -alh /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642
total 0
drwxrwxr-x. 2 omero-server omero-server  6 Jan  8 15:58 .
drwxrwxr-x. 5 omero-server omero-server 66 Jan  8 15:58 ..

lets try to delete .bfmemo and see if it fixes problem...

bash-4.2$ rm /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-14.425/.experiment_descriptor.xml.bfmemo

Now, we can no-longer view ANY images on http://localhost:1080/webclient/?show=plate-2705

    serverExceptionClass = ome.conditions.ResourceError
    message = Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-14.425/experiment_descriptor.xml

👎

After I delete the bfoptions file created above

$ rm /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-14.425/experiment_descriptor.xml.bfoptions

This allows images to be viewable again and a new .bfmemo is created

$ ls -alh /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-14.425
total 444K
drwxrwxr-x. 2 omero-server omero-server   47 Jan  8 16:41 .
drwxrwxr-x. 5 omero-server omero-server   66 Jan  8 15:58 ..
-rw-rw-r--. 1 omero-server omero-server 443K Jan  8 16:41 .experiment_descriptor.xml.bfmemo
will-moore commented 8 months ago

To get more stack trace, repeat.. As omero-server on idr-testing:omeroreadwrite

http://localhost:1080/webclient/?show=plate-2703 is currently viewable, except for last Wells

Write bfoptions... and check...

bash-4.2$ echo "scanr.skip_missing_wells=false" > "/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/experiment_descriptor.xml.bfoptions"

bash-4.2$ ls -alh /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/
total 108K
drwxrwxr-x.  3 omero-server omero-server  153 Jan 10 11:11 .
drwxrwxr-x. 72 omero-server omero-server 8.0K Nov 26  2015 ..
lrwxrwxrwx.  1 omero-server omero-server   97 Nov 26  2015 AcquisitionLog.dat -> /idr/filesets/idr0009-simpson-secretion/20150507-VSVG/VSVG/0305-09--2007-04-08/AcquisitionLog.dat
drwxrwxr-x.  2 omero-server omero-server  68K Nov 26  2015 data
lrwxrwxrwx.  1 omero-server omero-server  104 Nov 26  2015 experiment_descriptor.dat -> /idr/filesets/idr0009-simpson-secretion/20150507-VSVG/VSVG/0305-09--2007-04-08/experiment_descriptor.dat
lrwxrwxrwx.  1 omero-server omero-server  104 Nov 26  2015 experiment_descriptor.xml -> /idr/filesets/idr0009-simpson-secretion/20150507-VSVG/VSVG/0305-09--2007-04-08/experiment_descriptor.xml
-rw-r--r--.  1 omero-server omero-server   31 Jan 10 11:11 experiment_descriptor.xml.bfoptions

Delete bfmemo

rm /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/.experiment_descriptor.xml.bfmemo

Try to view any image from Plate in webclient... E.g. http://localhost:1080/webclient/?show=image-1315721 

2024-01-10 11:11:44,870 INFO  [                      omero.cmd.SessionI] (l.Server-7) Removed servant from adapter: 9505cb38-edc4-4c3e-8564-453be22fd71bomero.api.IQuery
2024-01-10 11:11:46,103 WARN  [   o.s.b.repo.ManagedReaderSecurityCheck] (.Server-24) reader for /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/experiment_descriptor.xml uses file from repository cdf35825-def1-4580-8d0b-9c349b8f78d6 that is not readable from database
2024-01-10 11:11:46,104 DEBUG [                   loci.formats.Memoizer] (.Server-24) start[1704885104459] time[1644] tag[loci.formats.Memoizer.setId]
2024-01-10 11:11:46,104 ERROR [         ome.io.bioformats.BfPixelBuffer] (.Server-24) Failed to instantiate BfPixelsWrapper with /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/experiment_descriptor.xml
2024-01-10 11:11:46,105 ERROR [                ome.io.nio.PixelsService] (.Server-24) Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/experiment_descriptor.xml
java.lang.RuntimeException: ome.conditions.SecurityViolation: reader for /data/OMERO/ManagedRepository/demo_2/2015-11/26/07-41-09.642/experiment_descriptor.xml uses file from repository cdf35825-def1-4580-8d0b-9c349b8f78d6 that is not readable from database
    at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:79)
    at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:124)
    at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:898)
    at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:653)
    at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:571)
    at ome.services.RenderingBean$12.doWork(RenderingBean.java:2205)
    at jdk.internal.reflect.GeneratedMethodAccessor282.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
will-moore commented 8 months ago

This is failing because the .bfoptions file is not registered in the DB. Attempting to create a .bfoptions OriginalFile via the OMERO API only allows it to be created in the /OMERO/Files/ location and not alongside the data in /OMERO/ManagedRepository/.

Try to use SQL instead...

addbfoptions.sql:

CREATE OR REPLACE FUNCTION add_origfile_to_fileset(
    fileset_id bigint,
    name character varying,
    uuid character varying)
  RETURNS integer AS
$BODY$
DECLARE
   new_event integer;
   old_owner integer;
   old_group integer;
   old_perms integer;
   new_file integer;
   files_count integer;
   prefix character varying;

BEGIN

    select _current_or_new_event() into new_event;
    select
        owner_id, group_id, permissions, templateprefix
     into
        old_owner, old_group, old_perms, prefix
     from fileset where id = fileset_id;

    select count(id) from filesetentry where fileset = fileset_id into files_count;

    insert into originalfile (id, permissions, creation_id, group_id, owner_id, update_id, mimetype, repo, path, name)
        values (nextval('seq_originalfile'), old_perms, new_event, old_group, old_owner, new_event,
            'application/octet-stream', 'cdf35825-def1-4580-8d0b-9c349b8f78d6', prefix, uuid || name)

            returning id into new_file;

    insert into filesetentry
          (id, permissions, creation_id, group_id, owner_id, update_id, fileset, originalfile, fileset_index, clientpath)
          values (nextval('seq_filesetentry'), old_perms, new_event, old_group, old_owner, new_event,
                  fileset_id, new_file, files_count, name);

    RETURN new_file;
END;
$BODY$
  LANGUAGE plpgsql VOLATILE;
$ psql -U omero -d idr -h $DBHOST -f addbfoptions.sql 
CREATE FUNCTION

Then:

$ psql -U omero -d idr -h $DBHOST -c "select add_origfile_to_fileset(19312, 'experiment_descriptor.xml.bfoptions', '9630ba1e-ed3a-42e3-9296-59ccf23a7039')"
 add_origfile_to_fileset 
-------------------------
                63726151
(1 row)
will-moore commented 8 months ago

on idr0125-pilot, as omero-server...

$ cat idr0009_filesets.csv
16604,demo_2/2015-11/26/07-41-14.425/
16605,demo_2/2015-11/26/07-41-25.452/
16603,demo_2/2015-11/26/07-41-09.642/
...
$ cat idr0009_filesets.csv | wc
   1035    1034   39126

We want to:

export $SECRET=9630ba1e-ed3a-42e3-9296-59ccf23a7039

for r in $(cat idr0009_filesets.csv); do
  fsid=$(echo $r | cut -d',' -f1)
  prefix=$(echo $r | cut -d',' -f2 | sed 's/.$//')
  echo "scanr.skip_missing_wells=false" > "/data/OMERO/ManagedRepository/$prefix/experiment_descriptor.xml.bfoptions";
  psql -U omero -d idr -h $DBHOST -c "select add_origfile_to_fileset($fsid, 'experiment_descriptor.xml.bfoptions', '$SECRET')"
  rm -f /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/$prefix/.experiment_descriptor.xml.bfmemo 
done
imagesc-bot commented 6 months ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/progressively-attach-timeframes-to-images-in-omero/93506/4

will-moore commented 5 months ago

Final test on pilot-idrngff...

idr0009_filesets.csv ``` 9509,demo_2/2015-09/23/10-40-23.554/ 12601,demo_2/2015-09/30/09-20-50.608/ 9512,demo_2/2015-09/23/10-48-58.762/ 9514,demo_2/2015-09/23/10-54-57.618/ 9515,demo_2/2015-09/23/11-01-09.292/ 9517,demo_2/2015-09/23/11-08-50.489/ 9519,demo_2/2015-09/23/11-14-58.128/ 9520,demo_2/2015-09/23/11-21-14.395/ 16856,demo_2/2015-12/08/09-05-47.246/ 9523,demo_2/2015-09/23/11-30-33.459/ 9525,demo_2/2015-09/23/11-38-36.949/ 9526,demo_2/2015-09/23/11-44-34.891/ 9528,demo_2/2015-09/23/11-51-00.298/ 9530,demo_2/2015-09/23/11-57-22.459/ 9531,demo_2/2015-09/23/12-04-54.373/ 9533,demo_2/2015-09/23/12-11-16.284/ 9535,demo_2/2015-09/23/12-17-27.426/ 16855,demo_2/2015-12/08/09-05-46.320/ 9537,demo_2/2015-09/23/12-26-19.536/ 16857,demo_2/2015-12/08/09-11-38.997/ 9540,demo_2/2015-09/23/12-37-00.491/ 16858,demo_2/2015-12/08/09-11-39.210/ 9543,demo_2/2015-09/23/12-46-11.342/ 16859,demo_2/2015-12/08/09-17-30.677/ 9546,demo_2/2015-09/23/12-56-29.725/ 16860,demo_2/2015-12/08/09-17-35.493/ 9550,demo_2/2015-09/23/13-06-15.559/ 9551,demo_2/2015-09/23/13-12-32.393/ 9553,demo_2/2015-09/23/13-18-46.851/ 9555,demo_2/2015-09/23/13-24-54.907/ 9556,demo_2/2015-09/23/13-31-00.882/ 16861,demo_2/2015-12/08/09-23-13.903/ 16862,demo_2/2015-12/08/09-23-20.244/ 9560,demo_2/2015-09/23/13-44-09.635/ 9562,demo_2/2015-09/23/13-50-22.163/ 9563,demo_2/2015-09/23/13-56-27.019/ 16863,demo_2/2015-12/08/09-28-52.890/ 16864,demo_2/2015-12/08/09-29-02.184/ 9567,demo_2/2015-09/23/14-08-35.348/ 9569,demo_2/2015-09/23/14-14-48.040/ 9571,demo_2/2015-09/23/14-21-09.912/ 9572,demo_2/2015-09/23/14-27-22.195/ 9574,demo_2/2015-09/23/14-33-21.671/ 9575,demo_2/2015-09/23/14-39-02.969/ 9577,demo_2/2015-09/23/14-46-01.705/ 9579,demo_2/2015-09/23/14-51-43.357/ 9580,demo_2/2015-09/23/14-57-11.669/ 9582,demo_2/2015-09/23/15-03-00.076/ 9583,demo_2/2015-09/23/15-08-33.500/ 9584,demo_2/2015-09/23/15-14-30.171/ 16865,demo_2/2015-12/08/09-34-34.991/ 9586,demo_2/2015-09/23/15-22-50.971/ 9589,demo_2/2015-09/23/15-28-24.458/ 16866,demo_2/2015-12/08/09-34-48.788/ 9591,demo_2/2015-09/23/15-36-03.690/ 16867,demo_2/2015-12/08/09-40-11.545/ 9594,demo_2/2015-09/23/15-44-31.181/ 9595,demo_2/2015-09/23/15-49-57.569/ 9596,demo_2/2015-09/23/15-55-33.745/ 9597,demo_2/2015-09/23/16-01-27.191/ 9598,demo_2/2015-09/23/16-07-03.326/ 9599,demo_2/2015-09/23/16-12-35.026/ 16868,demo_2/2015-12/08/09-40-23.421/ 9601,demo_2/2015-09/23/16-20-25.131/ 16869,demo_2/2015-12/08/09-45-43.657/ 9603,demo_2/2015-09/23/16-28-02.278/ 9604,demo_2/2015-09/23/16-33-27.678/ 16870,demo_2/2015-12/08/09-45-57.047/ 16871,demo_2/2015-12/08/09-51-21.577/ 16872,demo_2/2015-12/08/09-51-28.186/ 9608,demo_2/2015-09/23/16-45-19.289/ 9609,demo_2/2015-09/23/16-50-30.778/ 16873,demo_2/2015-12/08/09-57-02.089/ 9611,demo_2/2015-09/23/16-57-53.411/ 16874,demo_2/2015-12/08/09-57-04.588/ 9613,demo_2/2015-09/23/17-05-27.903/ 16875,demo_2/2015-12/08/10-02-37.839/ 9616,demo_2/2015-09/23/17-14-38.441/ 16876,demo_2/2015-12/08/10-02-44.523/ 9618,demo_2/2015-09/23/17-22-30.321/ 16877,demo_2/2015-12/08/10-08-11.312/ 9620,demo_2/2015-09/23/17-30-21.444/ 9621,demo_2/2015-09/23/17-36-19.095/ 16878,demo_2/2015-12/08/10-08-16.143/ 16879,demo_2/2015-12/08/10-13-46.708/ 16880,demo_2/2015-12/08/10-13-46.714/ 16881,demo_2/2015-12/08/10-19-17.282/ 9626,demo_2/2015-09/23/17-51-55.885/ 9627,demo_2/2015-09/23/17-57-17.164/ 9628,demo_2/2015-09/23/18-02-40.808/ 16882,demo_2/2015-12/08/10-19-18.592/ 9630,demo_2/2015-09/23/18-11-04.342/ 9631,demo_2/2015-09/23/18-16-52.382/ 9632,demo_2/2015-09/23/18-22-43.226/ 9633,demo_2/2015-09/23/18-28-36.740/ 9634,demo_2/2015-09/23/18-34-31.165/ 16883,demo_2/2015-12/08/10-24-49.087/ 9636,demo_2/2015-09/23/18-43-20.871/ 16884,demo_2/2015-12/08/10-24-52.313/ 16885,demo_2/2015-12/08/10-30-21.192/ 9639,demo_2/2015-09/23/18-55-02.988/ 9640,demo_2/2015-09/23/19-00-54.951/ 16886,demo_2/2015-12/08/10-30-28.181/ 9642,demo_2/2015-09/23/19-09-42.636/ 16887,demo_2/2015-12/08/10-35-52.002/ 16888,demo_2/2015-12/08/10-35-53.352/ 9645,demo_2/2015-09/23/19-21-05.741/ 16889,demo_2/2015-12/08/10-41-21.964/ 9647,demo_2/2015-09/23/19-29-49.047/ 9648,demo_2/2015-09/23/19-35-34.256/ 16890,demo_2/2015-12/08/10-41-23.303/ 9650,demo_2/2015-09/23/19-44-22.936/ 16891,demo_2/2015-12/08/10-46-51.096/ 16892,demo_2/2015-12/08/10-46-56.319/ 16893,demo_2/2015-12/08/10-52-22.797/ 9654,demo_2/2015-09/23/19-58-57.800/ 9655,demo_2/2015-09/23/20-04-53.704/ 16894,demo_2/2015-12/08/10-52-27.955/ 16895,demo_2/2015-12/08/10-57-57.026/ 9658,demo_2/2015-09/23/20-16-32.372/ 9659,demo_2/2015-09/23/20-22-20.890/ 9660,demo_2/2015-09/23/20-28-44.252/ 16896,demo_2/2015-12/08/10-57-57.441/ 16897,demo_2/2015-12/08/11-03-29.309/ 9663,demo_2/2015-09/23/20-40-02.979/ 9664,demo_2/2015-09/23/20-45-24.739/ 16898,demo_2/2015-12/08/11-03-31.426/ 9666,demo_2/2015-09/23/20-53-54.614/ 16899,demo_2/2015-12/08/11-09-00.864/ 9668,demo_2/2015-09/23/21-02-27.329/ 9669,demo_2/2015-09/23/21-08-01.095/ 16900,demo_2/2015-12/08/11-09-06.864/ 9671,demo_2/2015-09/23/21-16-22.538/ 16901,demo_2/2015-12/08/11-14-39.983/ 9673,demo_2/2015-09/23/21-24-47.651/ 9674,demo_2/2015-09/23/21-30-25.719/ 9675,demo_2/2015-09/23/21-35-59.714/ 16902,demo_2/2015-12/08/11-14-41.475/ 16903,demo_2/2015-12/08/11-20-16.804/ 16904,demo_2/2015-12/08/11-20-17.754/ 9680,demo_2/2015-09/23/21-51-22.551/ 16906,demo_2/2015-12/08/11-25-51.487/ 9682,demo_2/2015-09/23/21-59-40.805/ 16905,demo_2/2015-12/08/11-25-50.848/ 9684,demo_2/2015-09/23/22-07-43.970/ 9685,demo_2/2015-09/23/22-13-06.897/ 9686,demo_2/2015-09/23/22-18-24.109/ 16907,demo_2/2015-12/08/11-31-21.270/ 16908,demo_2/2015-12/08/11-31-23.994/ 16909,demo_2/2015-12/08/11-36-49.911/ 9690,demo_2/2015-09/23/22-32-07.915/ 9691,demo_2/2015-09/23/22-37-54.790/ 9692,demo_2/2015-09/23/22-43-54.114/ 16910,demo_2/2015-12/08/11-36-52.778/ 16911,demo_2/2015-12/08/11-42-30.279/ 9695,demo_2/2015-09/23/22-55-31.239/ 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12818,demo_2/2015-10/01/01-48-57.412/ 12819,demo_2/2015-10/01/01-55-01.937/ 12820,demo_2/2015-10/01/02-01-24.647/ 12822,demo_2/2015-10/01/02-07-51.811/ 12823,demo_2/2015-10/01/02-13-50.327/ 12824,demo_2/2015-10/01/02-19-54.893/ 12825,demo_2/2015-10/01/02-26-20.547/ 12827,demo_2/2015-10/01/02-32-37.278/ 12828,demo_2/2015-10/01/02-38-56.401/ 12829,demo_2/2015-10/01/02-44-55.118/ 12830,demo_2/2015-10/01/02-51-49.026/ 12832,demo_2/2015-10/01/02-58-15.406/ 12833,demo_2/2015-10/01/03-04-30.710/ 12834,demo_2/2015-10/01/03-11-11.882/ 12835,demo_2/2015-10/01/03-17-51.071/ 12837,demo_2/2015-10/01/03-24-33.923/ 12838,demo_2/2015-10/01/03-31-09.809/ 12839,demo_2/2015-10/01/03-37-36.796/ 12840,demo_2/2015-10/01/03-43-51.218/ 12842,demo_2/2015-10/01/03-50-21.007/ 12843,demo_2/2015-10/01/03-56-27.761/ 12844,demo_2/2015-10/01/04-02-11.982/ 12845,demo_2/2015-10/01/04-08-35.558/ 12846,demo_2/2015-10/01/04-15-11.925/ 12848,demo_2/2015-10/01/04-21-49.274/ 12849,demo_2/2015-10/01/04-28-21.132/ 12850,demo_2/2015-10/01/04-34-49.036/ 12851,demo_2/2015-10/01/04-41-40.328/ 12853,demo_2/2015-10/01/04-47-46.641/ 12854,demo_2/2015-10/01/04-54-02.744/ 12855,demo_2/2015-10/01/05-00-21.412/ 12856,demo_2/2015-10/01/05-06-39.588/ 12858,demo_2/2015-10/01/05-13-04.729/ 12859,demo_2/2015-10/01/05-19-16.210/ 12860,demo_2/2015-10/01/05-25-27.082/ 12861,demo_2/2015-10/01/05-31-46.907/ 12863,demo_2/2015-10/01/05-38-43.631/ 12864,demo_2/2015-10/01/05-45-04.161/ 12865,demo_2/2015-10/01/05-51-23.052/ 12866,demo_2/2015-10/01/05-57-23.279/ 12868,demo_2/2015-10/01/06-03-32.758/ 12869,demo_2/2015-10/01/06-09-46.616/ 12870,demo_2/2015-10/01/06-15-48.792/ 12871,demo_2/2015-10/01/06-21-31.936/ 12872,demo_2/2015-10/01/06-27-49.537/ 12874,demo_2/2015-10/01/06-34-15.755/ 12875,demo_2/2015-10/01/06-40-14.572/ 12876,demo_2/2015-10/01/06-46-22.320/ 12877,demo_2/2015-10/01/06-52-52.900/ 12957,demo_2/2015-10/01/09-25-07.830/ 12959,demo_2/2015-10/01/09-31-12.185/ 12960,demo_2/2015-10/01/09-37-17.960/ 12961,demo_2/2015-10/01/09-43-34.542/ 12962,demo_2/2015-10/01/09-49-59.363/ 12964,demo_2/2015-10/01/09-56-34.784/ 12965,demo_2/2015-10/01/10-02-43.718/ 12967,demo_2/2015-10/01/10-08-51.888/ 12968,demo_2/2015-10/01/10-15-12.706/ 12969,demo_2/2015-10/01/10-21-53.457/ 12971,demo_2/2015-10/01/10-28-30.950/ 12972,demo_2/2015-10/01/10-34-47.988/ 12974,demo_2/2015-10/01/10-41-09.573/ 12975,demo_2/2015-10/01/10-47-40.543/ 12977,demo_2/2015-10/01/10-54-24.770/ 12978,demo_2/2015-10/01/11-00-31.953/ 12979,demo_2/2015-10/01/11-06-34.480/ 12981,demo_2/2015-10/01/11-12-47.351/ 12983,demo_2/2015-10/01/11-19-03.415/ 12984,demo_2/2015-10/01/11-25-00.635/ 12985,demo_2/2015-10/01/11-30-54.893/ 12987,demo_2/2015-10/01/11-36-57.917/ 12988,demo_2/2015-10/01/11-43-07.629/ 12991,demo_2/2015-10/01/11-49-37.590/ 12992,demo_2/2015-10/01/11-55-35.775/ 12993,demo_2/2015-10/01/12-01-47.858/ 12995,demo_2/2015-10/01/12-07-58.931/ 12997,demo_2/2015-10/01/12-14-14.894/ 12998,demo_2/2015-10/01/12-20-38.683/ 12999,demo_2/2015-10/01/12-26-40.962/ 13000,demo_2/2015-10/01/12-33-02.962/ 13003,demo_2/2015-10/01/12-39-31.682/ 13005,demo_2/2015-10/01/12-45-52.407/ 13006,demo_2/2015-10/01/12-52-14.938/ 13008,demo_2/2015-10/01/12-58-23.595/ 13010,demo_2/2015-10/01/13-05-00.240/ 13014,demo_2/2015-10/01/13-11-34.045/ 13015,demo_2/2015-10/01/13-17-47.134/ 13017,demo_2/2015-10/01/13-23-53.558/ 13019,demo_2/2015-10/01/13-30-22.751/ 13022,demo_2/2015-10/01/13-36-46.207/ 13024,demo_2/2015-10/01/13-43-02.405/ 13026,demo_2/2015-10/01/13-49-11.182/ 13028,demo_2/2015-10/01/13-55-30.764/ 13031,demo_2/2015-10/01/14-01-45.865/ 13032,demo_2/2015-10/01/14-07-37.815/ 13035,demo_2/2015-10/01/14-13-32.004/ 13037,demo_2/2015-10/01/14-19-29.507/ 13039,demo_2/2015-10/01/14-25-43.993/ 13041,demo_2/2015-10/01/14-32-04.428/ 13044,demo_2/2015-10/01/14-38-24.645/ 13046,demo_2/2015-10/01/14-44-33.626/ 13048,demo_2/2015-10/01/14-51-12.815/ 13050,demo_2/2015-10/01/14-57-02.122/ 13052,demo_2/2015-10/01/15-03-01.218/ 13055,demo_2/2015-10/01/15-09-04.741/ 13057,demo_2/2015-10/01/15-15-13.789/ 13059,demo_2/2015-10/01/15-21-04.542/ 13061,demo_2/2015-10/01/15-26-53.667/ 13063,demo_2/2015-10/01/15-33-23.571/ 13066,demo_2/2015-10/01/15-39-51.458/ 13068,demo_2/2015-10/01/15-46-23.961/ 13070,demo_2/2015-10/01/15-52-27.816/ 13072,demo_2/2015-10/01/15-58-46.387/ 13075,demo_2/2015-10/01/16-04-52.656/ 13076,demo_2/2015-10/01/16-11-26.677/ 13079,demo_2/2015-10/01/16-17-39.028/ 13081,demo_2/2015-10/01/16-23-53.300/ 13083,demo_2/2015-10/01/16-30-14.591/ 13085,demo_2/2015-10/01/16-36-42.872/ 13088,demo_2/2015-10/01/16-43-02.538/ 13090,demo_2/2015-10/01/16-48-56.648/ 13092,demo_2/2015-10/01/16-55-27.191/ 13093,demo_2/2015-10/01/17-02-14.734/ 13097,demo_2/2015-10/01/17-08-24.492/ 13099,demo_2/2015-10/01/17-14-49.374/ 13101,demo_2/2015-10/01/17-21-28.449/ 13102,demo_2/2015-10/01/17-28-07.582/ 13106,demo_2/2015-10/01/17-33-34.988/ 13108,demo_2/2015-10/01/17-39-25.063/ 13109,demo_2/2015-10/01/17-45-20.599/ 13111,demo_2/2015-10/01/17-51-21.461/ 13114,demo_2/2015-10/01/17-57-26.988/ 13117,demo_2/2015-10/01/18-03-20.340/ 13118,demo_2/2015-10/01/18-09-35.509/ 13120,demo_2/2015-10/01/18-15-50.039/ 13122,demo_2/2015-10/01/18-22-00.848/ 13127,demo_2/2015-10/01/18-27-56.541/ 13129,demo_2/2015-10/01/18-34-16.508/ 13131,demo_2/2015-10/01/18-40-21.219/ 13133,demo_2/2015-10/01/18-46-39.586/ 13136,demo_2/2015-10/01/18-52-31.127/ 13137,demo_2/2015-10/01/18-58-24.547/ 13140,demo_2/2015-10/01/19-04-51.379/ 13142,demo_2/2015-10/01/19-11-11.349/ 13145,demo_2/2015-10/01/19-16-50.191/ 13146,demo_2/2015-10/01/19-22-53.369/ 13149,demo_2/2015-10/01/19-28-43.372/ 13151,demo_2/2015-10/01/19-34-53.225/ 13154,demo_2/2015-10/01/19-41-14.268/ 13155,demo_2/2015-10/01/19-47-48.732/ 13157,demo_2/2015-10/01/19-54-18.295/ 13160,demo_2/2015-10/01/20-00-54.981/ 13163,demo_2/2015-10/01/20-07-23.969/ 13164,demo_2/2015-10/01/20-13-58.818/ 13166,demo_2/2015-10/01/20-20-06.842/ 13168,demo_2/2015-10/01/20-26-18.235/ 13171,demo_2/2015-10/01/20-33-05.794/ 13174,demo_2/2015-10/01/20-39-41.075/ 13175,demo_2/2015-10/01/20-46-11.133/ 13177,demo_2/2015-10/01/20-52-46.407/ 13180,demo_2/2015-10/01/20-59-41.235/ 13183,demo_2/2015-10/01/21-06-00.474/ 13184,demo_2/2015-10/01/21-12-10.947/ 13186,demo_2/2015-10/01/21-18-22.255/ 13188,demo_2/2015-10/01/21-24-36.691/ 13192,demo_2/2015-10/01/21-30-38.021/ 13193,demo_2/2015-10/01/21-36-47.397/ 13195,demo_2/2015-10/01/21-42-41.795/ 13197,demo_2/2015-10/01/21-48-53.810/ 13201,demo_2/2015-10/01/21-54-46.570/ 13202,demo_2/2015-10/01/22-00-54.141/ 13204,demo_2/2015-10/01/22-06-43.369/ 13206,demo_2/2015-10/01/22-12-43.783/ 13208,demo_2/2015-10/01/22-19-19.107/ 13211,demo_2/2015-10/01/22-25-16.630/ 13213,demo_2/2015-10/01/22-31-25.311/ 13215,demo_2/2015-10/01/22-37-39.318/ 13217,demo_2/2015-10/01/22-44-13.076/ 13219,demo_2/2015-10/01/22-50-28.612/ 13222,demo_2/2015-10/01/22-56-47.549/ 13224,demo_2/2015-10/01/23-02-39.399/ 13226,demo_2/2015-10/01/23-08-47.367/ 13228,demo_2/2015-10/01/23-14-28.943/ 13230,demo_2/2015-10/01/23-20-39.090/ 16597,demo_2/2015-11/26/07-22-16.896/ 16598,demo_2/2015-11/26/07-35-04.370/ 16600,demo_2/2015-11/26/07-35-04.899/ 16599,demo_2/2015-11/26/07-35-04.628/ 16601,demo_2/2015-11/26/07-35-05.437/ 16602,demo_2/2015-11/26/07-41-03.013/ 16603,demo_2/2015-11/26/07-41-09.642/ 16604,demo_2/2015-11/26/07-41-14.425/ 16605,demo_2/2015-11/26/07-41-25.452/ 16607,demo_2/2015-11/26/07-47-36.451/ 16606,demo_2/2015-11/26/07-47-36.244/ 16608,demo_2/2015-11/26/07-47-40.196/ 16609,demo_2/2015-11/26/07-47-47.588/ 16610,demo_2/2015-11/26/07-54-05.252/ 16611,demo_2/2015-11/26/07-54-13.723/ 16612,demo_2/2015-11/26/07-54-16.504/ 16613,demo_2/2015-11/26/07-54-21.235/ 16614,demo_2/2015-11/26/08-00-49.390/ 16615,demo_2/2015-11/26/08-00-51.649/ 16616,demo_2/2015-11/26/08-00-58.131/ 16617,demo_2/2015-11/26/08-00-59.868/ 16619,demo_2/2015-11/26/08-07-48.292/ 16618,demo_2/2015-11/26/08-07-47.628/ 16620,demo_2/2015-11/26/08-07-50.974/ 16621,demo_2/2015-11/26/08-07-52.552/ 16622,demo_2/2015-11/26/08-13-40.451/ 16623,demo_2/2015-11/26/08-13-44.940/ 18252,demo_2/2015-12/09/11-54-23.222/ 16624,demo_2/2015-11/26/08-13-51.716/ 16625,demo_2/2015-11/26/08-14-17.510/ 16626,demo_2/2015-11/26/08-19-27.833/ 16627,demo_2/2015-11/26/08-19-35.553/ 16628,demo_2/2015-11/26/08-19-41.906/ 16629,demo_2/2015-11/26/08-20-14.859/ 16630,demo_2/2015-11/26/08-25-10.606/ 16631,demo_2/2015-11/26/08-25-15.256/ 16632,demo_2/2015-11/26/08-25-30.263/ 16633,demo_2/2015-11/26/08-25-56.249/ 16634,demo_2/2015-11/26/08-31-01.323/ 16635,demo_2/2015-11/26/08-31-10.605/ 16636,demo_2/2015-11/26/08-31-25.703/ 16637,demo_2/2015-11/26/08-31-41.587/ 16638,demo_2/2015-11/26/08-36-51.966/ 16639,demo_2/2015-11/26/08-37-07.891/ 16640,demo_2/2015-11/26/08-37-38.389/ 16641,demo_2/2015-11/26/08-37-46.199/ 16642,demo_2/2015-11/26/08-42-46.804/ 16643,demo_2/2015-11/26/08-43-04.443/ 16644,demo_2/2015-11/26/08-43-41.537/ 16645,demo_2/2015-11/26/08-43-44.114/ 16646,demo_2/2015-11/26/08-48-34.561/ 16647,demo_2/2015-11/26/08-49-00.896/ 16648,demo_2/2015-11/26/08-50-34.647/ 16649,demo_2/2015-11/26/08-50-34.720/ 16650,demo_2/2015-11/26/08-54-17.561/ 16651,demo_2/2015-11/26/08-54-50.012/ 16652,demo_2/2015-11/26/08-56-30.469/ 16653,demo_2/2015-11/26/08-56-36.178/ 16654,demo_2/2015-11/26/09-00-45.791/ 16655,demo_2/2015-11/26/09-00-59.336/ 16656,demo_2/2015-11/26/09-02-28.876/ 16657,demo_2/2015-11/26/09-02-37.479/ 16658,demo_2/2015-11/26/09-06-34.598/ 16659,demo_2/2015-11/26/09-06-57.037/ 16660,demo_2/2015-11/26/09-09-37.246/ 16661,demo_2/2015-11/26/09-09-45.135/ 16662,demo_2/2015-11/26/09-12-22.073/ 16663,demo_2/2015-11/26/09-12-37.788/ 16664,demo_2/2015-11/26/09-15-28.047/ 16665,demo_2/2015-11/26/09-15-36.785/ ``` 
wc idr0009_filesets.csv 
 1034  1034 39125 idr0009_filesets.csv

vi addbfoptions.sql   # see above

$ psql -U omero -d idr -h $DBHOST -f addbfoptions.sql 
CREATE FUNCTION

$ export SECRET=41fe4790-5848-4ae9-bc08-c84157af8191

for r in $(cat idr0009_filesets.csv); do
  fsid=$(echo $r | cut -d',' -f1)
  prefix=$(echo $r | cut -d',' -f2 | sed 's/.$//')
  echo "scanr.skip_missing_wells=false" > "/data/OMERO/ManagedRepository/$prefix/experiment_descriptor.xml.bfoptions";
  psql -U omero -d idr -h $DBHOST -c "select add_origfile_to_fileset($fsid, 'experiment_descriptor.xml.bfoptions', '$SECRET')"
  rm -f /data/OMERO/BioFormatsCache/data/OMERO/ManagedRepository/$prefix/.experiment_descriptor.xml.bfmemo 
done

All images viewable once memo files regenerated (quite quick in webclient)

will-moore commented 5 months ago

Josh "SQL looks reasonable enough. I'd say we should really move this to a server method long-term though. (I'd probably have done max()+1 rather than select count(id) from filesetentry where fileset = fileset_id into files_count; but that's likely not too important assuming there aren't any usedFiles list with nulls)