I am getting an unexpected problem, I say this because when I ran my pipeline with version
4.0.4 it worked well; now with new images I built a new metadata file (
.csv) in the same way as before, and installed the new version
4.0.7. The issue is that now I can’t extract the metadata from the file. I only have two variables in the file
file_name to match the
biological_group to make groups in the block
I spent two hours looking for typos, and I couldn’t find any, also ran as Admin did not solve the issue, and finally I thought on looking the command line and it says:
Exception in thread "Thread-0" java.io.IOException: Key, "?file_name", is missing from CSV header.at org.cellprofiler.imageset.ImportedMetadataExtractor.<init>(ImportedMetadataExtractor.java:111)
What is odd to me is that the variables are detected (since I can select it in
Metadata block), but it is not read: says “nan” in
Groups. So I change the grouping from a name (“control”, or “treatment”) to a number (1 or 2), and the problem persisted. But what is even stranger is that the
file_name is matched with
FileLocation, without issue, which, to me, means that the file in being read and the observation in
file_name are there and without typos.
What do you think that I might be doing wrong here?
- What stops you from proceeding?
Metadatablock is not reading the metadata (as before) from a
- What have you tried already?
It worked in version
4.0.7tested the same pipeline and the same files and it did not work
- Have you found any related forum topics? If so, cross-link them.
No, at least not yet.
Thank you in advance.