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idr0009 ScanR missing Wells #684

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will-moore opened this issue Jan 10, 2024 · 7 comments
Open

idr0009 ScanR missing Wells #684

will-moore opened this issue Jan 10, 2024 · 7 comments

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@will-moore
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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
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Tested this (originally posted at #675 (comment))...

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
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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 will-moore moved this to convert all data to NGFF in NGFF conversion Jan 10, 2024
@will-moore
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will-moore commented Jan 10, 2024 •
edited
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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
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will-moore commented Jan 11, 2024 •
edited
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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:

  • create the bfoptions file (in the Fileset directory)
  • add that file to the Fileset (NB: fails if OriginalFile already exists)
  • delete the .bfmemo
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

@will-moore will-moore mentioned this issue Jan 15, 2024
Open
14 tasks
@imagesc-bot
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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
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will-moore commented Apr 25, 2024 •
edited
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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/
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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
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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)

@will-moore will-moore mentioned this issue May 1, 2024
Open
@will-moore will-moore mentioned this issue May 21, 2024
Open
15 tasks
@will-moore will-moore mentioned this issue Jun 6, 2024
Merged
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