Comments (3)
When looking into the usage of Pixels path/name in IDR, I think I checked a bunch of Filesets in IDR to see if the first File matched the path/name in Pixels and found that there were differences in many cases. Unfortunately I can't remember where I documented that...
Also I don't know if Bio-Formats would have behaved differently if the different path/name was used in setId().
from openmicroscopy.
Ah - I found it: IDR/idr-metadata#660 (comment)
So, testing 1 image from each study in IDR (to get a good mix of formats etc) it looks like there were 22 studies where the Pixels path/name didn't match the first OriginalFile from the Fileset.
from openmicroscopy.
Thanks @will-moore looking at your list of mismatches, all of these examples are multi-file & multi-folder file formats, primarily HCS but not only. Also from a quick search using the IDR UI, it seems that the first FilesetEntry.clientPath
is matches Pixels.path
and Pixels.name
. Both of these observations are consistent with my expectations based on preliminary investigation.
Also I don't know if Bio-Formats would have behaved differently if the different path/name was used in setId().
Unfortunately, the answer here is "it depends". In the worst case scenario, Bio-Formats would throw an UnknownFormatException
on setId
.
As a next step here my plan is to write a pre-check SQL script that iterates through all the Fileset
in a database and tries to match the first FilesetEntry
with any of the OriginalFile
using fileset.clientPath
and originalfile.{path,name}
. We should be able to run this script against the IDR database and other OMERO databases to give us a feeling on whether we can fix these links in an authoritative manner.
from openmicroscopy.
Related Issues (20)
- failed upgrade to Omero5.5 - Ice 3.6 not found HOT 2
- More non-parallel test assumptions
- omero db script → psql: identifiers truncated
- Document Python logging properties
- Manage services from the omero settings HOT 1
- missing OMERO.insight-5.4.10-ice36-b105-linux.zip HOT 4
- AdminService load Experimenters and Groups options with GroupExperimenterMap
- Improve performance of graph operations. HOT 2
- Annotations displaced when opening saved qpdata file HOT 1
- Alternate gradle/maven artifactory location? HOT 3
- CZI file Exposure time HOT 4
- Fix JSON API JavaScript login example HOT 1
- Increase the usage of compound assignment operators HOT 1
- Release process review HOT 4
- OMERO.server: JDK 17 support HOT 1
- Update the OMERO model and API to represent and handle archived data
- Unpin numpy<2 HOT 2
- omero.LockTimeout exception on "omero admin email" HOT 7
- Distribution contents regression with Ivy 2.5.2 HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from openmicroscopy.