User Story #6309 (new)
Opened 13 years ago
Last modified 8 years ago
Bio-Formats to provide strict and lax validation
| Reported by: | ajpatterson | Owned by: | |
|---|---|---|---|
| Priority: | minor | Milestone: | Unscheduled |
| Component: | Bio-Formats | Keywords: | schema, validator |
| Cc: | jamoore, mlinkert | Story Points: | n.a. |
| Sprint: | n.a. | Importance: | n.a. |
| Total Remaining Time: | n.a. | Estimated Remaining Time: | n.a. |
Description (last modified by ajpatterson)
Add support to bio-formats that will allow validation of ome files. As well as reading a completely valid ome structure, include option to find a valid ome structure hidden with other data.
The idea is to add validation code to bio-formats. This will include validation of the structure of the data (is it good ome-xml?), but also validation of the values inside the structure (is the data complete? can I find all the tiff frames needed? does it make sense as an image?). There is a small bit of this in the old online validator but it would be better to re-write it bio-formats. This could then be exposed via bf-tools and also form the backend to a new online validator.
The solution should also cope with embeded ome-xml, e.g. <Foo><OME>...</OME></Foo>
Change History (11)
comment:1 Changed 13 years ago by ajpatterson
- Description modified (diff)
comment:2 Changed 13 years ago by ajpatterson
- Component changed from General to Bio-Formats
- Owner set to mlinkert-x
comment:3 Changed 13 years ago by ajpatterson
- Cc jmoore added
comment:4 Changed 13 years ago by ajpatterson
- Milestone changed from Unscheduled to OMERO-Beta4.3.2
comment:5 Changed 13 years ago by jburel
- Cc mlinkert-x added
- Owner mlinkert-x deleted
comment:6 Changed 13 years ago by jburel
- Milestone changed from OMERO-Beta4.3.2 to Unscheduled
comment:7 Changed 11 years ago by ajpatterson
- Keywords schema validator added
comment:8 Changed 11 years ago by ajpatterson
- Milestone changed from Unscheduled to OMERO-5
comment:9 Changed 11 years ago by ajpatterson
- Description modified (diff)
comment:10 Changed 8 years ago by jamoore
- Milestone changed from 5.x to Unscheduled
comment:11 Changed 8 years ago by sbesson
https://github.com/openmicroscopy/bioformats/pull/2456 might be the first step here.
Need to consider for validation work in 4.3.2 milestone.