Open chris-allan opened 7 years ago
The length restriction was previously discussed but not removed this will require some db adjustments see https://trac.openmicroscopy.org/ome/ticket/11894
http://trac.openmicroscopy.org/ome/ticket/11894 discusses the length restrictions. Happy to switch to TEXT
in the DB any properties that we like. (See distinction between string
and text
on http://www.openmicroscopy.org/site/support/omero5.3-staging/developers/Model/EveryObject.html) Perhaps one may reasonably prioritize properties for which the corresponding OME-XML attribute is already of unrestricted length.
Current "named" objects, which consequently have a character varying database column of length 255 reserved to store a name
property, are as follows:
Image
OriginalFile
StageLabel
Project
Dataset
Folder
(yes, @sbesson :))Namespace
(also displayname
)Screen
Plate
Exceptions to this include ExperimenterGroup
which is not "named" but has a name
character varying database column of length 255.
Update on this design issue:
Plate
name read by Bio-Formats at import timea few threads have been recently raised recently about the remaining issue i.e. trusting the Image
name read by Bio-Formats at import time
for non-screen data, idr0040 is an example where the image name (read by https://github.com/openmicroscopy/bioformats/pull/3092) needs to be overriden by -n
option via a bulk file
for HCS data, see http://lists.openmicroscopy.org.uk/pipermail/ome-users/2018-April/007001.html
Created [trello] ignores plate names in naming fields for the issue in PixelsProcessor
relating to the above community thread.
See also https://www.openmicroscopy.org/community/viewtopic.php?f=4&p=19976#p19976 for another community use case where allowing to read the ImageName from Bio-Formats in the non-HCS behavior would be useful.
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/upload-issue-with-metadata-ome-xml-companion-file/59290/8
The issue
The current state of how
Image
andPlate
name are treated in the importer and the historical lack of trust put in the metadata coming out of Bio-Formats is becoming a problem.With respect to
Plate
name, unless it is explicitly chosen by the user using OMERO.cli, it will be set to the Bio-Formats target filename and anyPlate
name metadata is ignored. This is an issue when the desired name is deep within the metadata, requiring users to perform their own metadata extraction in order to set the name. It is also particularly problematic when thePlate
count being imported is large effectively necessitating that a user write shell scripts in order to import their data correctly.The same holds true for a singular
Image
. If theImage
is part of a multi-image fileset (MIF) its series number is used as part of the name and any Bio-Formats name metadata is ignored. This is an issue when, using images of the digital pathology domain as an example, eachImage
has a self describing name which ends up effectively being lost.History and state of play
The processor that enforces the aforementioned rule on
Image
:For OMERO 5.0.0 (openmicroscopy/openmicroscopy#1710) the filename, rather than the absolute path became used as the default name unless the user specifies one explicitly.
This is also when the Bio-Formats
Image
name metadata began being ignored for multi-image filesets. The rationale for this is not completely clear to me. Length restrictions were also put in place, substituting ellipses when the name is longer than 255 characters.From OMERO 4.3.0, (openmicroscopy/openmicroscopy@98691605), the user specified name has defaulted to the absolute path and became just the filename in openmicroscopy/openmicroscopy#1710. The rationale, albeit not a particularly thorough, is outlined in this corresponding ticket:
The processor that enforces the aforementioned rule on
Plate
:Also for OMERO 5.0.0 (openmicroscopy/openmicroscopy#577; openmicroscopy/openmicroscopy@92ec095b), the user specified
Image
andPlate
name were unified. This had the potential unintended side effect, as the user specifiedImage
name was the absolute path and became just the filename in openmicroscopy/openmicroscopy#1710, of always setting a user specifiedPlate
name regardless of whether the user had conciously made that decision or not.From OMERO 4.2.1 (openmicroscopy/openmicroscopy@87db20ab), a user specified
Plate
name has been possible.Current work on the issue
Suggestions for moving forward
OMERO 5.2.x
No change.
OMERO 5.3.x
Plate
name metadata provided by Bio-Formats unless the user has specifically overriden it. If such metadata is missing or blank use the current default: filename.Image
name metadata provided by Bio-Formats when imported under multi-image fileset (MIF) conditions. If such metadata is missing or blank use the current default: filename./cc @jburel, @joshmoore, @sbesson, @melissa-linkert, @mtbc, @will-moore
/cc @emilroz
Edits
Mon 19 Sep 2016 16:23:36 BST
: Add ongoing work from @melissa-linkert, @joshmoore, @mtbcWed 21 Sep 2016 09:22:21 BST
: Reference to ongoing work on relaxing length restrictions on names