Sébastien Besson

Agreed, and this might be a side-effect of the way the process was terminated. Does the following work? ``` $ sudo umount /bia-integrator-data $ sudo /opt/goofys --endpoint https://uk1s3.embassy.ebi.ac.uk/ -o allow_other...

A few thoughts: 1- try to pass `-f` to force unmount 2- try to stop the processes that might be accessing some of the data e.g. `omero-server`

Externally, it should be possible to extend https://github.com/IDR/upptime to monitor specific endpoints testing images available via `goofys` e.g. https://github.com/IDR/upptime/blob/9932b00f1b53c1e0aa53ac1ed6c715bde2fc49cc/.upptimerc.yml#L84-L85 Internally, the best strategy would be to make use Prometheus e.g....

There are a series of issues we might need to review here. For reference, the source data corresponding to the example above is https://ftp.ebi.ac.uk/pub/databases/IDR/idr0001-graml-sysgro/20151116-verified/JL_120731_S6A/. As can be seen above, there...

> Error is raised at https://github.com/ome/omero-romio/blob/1d30fafc4e06c5511cfbb24c25a753925ffb2eb4/src/main/java/ome/io/bioformats/BfPixelBuffer.java#L79 but that's not where the ClassCastException comes from. I suspect the error comes from the underlying reader and is rethrown from the Bio-Formats pixel...

> Plates converted are ~47 GB so we only have space to convert 1 plate on each of pilot-zarr1-dev and pilot-zarr2-dev`. > > ``` > (base) [wmoore@pilot-zarr1-dev ~]$ df -h...

Looks like I had made some progress on this conversion in the same way as https://github.com/IDR/idr-metadata/issues/649 using the following script ```python import os sourcedir="/uod/idr/filesets/idr0035-caie-drugresponse/images" targetdir='/data/idr0035/sources/' zarrdir="/data/idr0035/zarr/" bf2raw_exec = "/opt/bioformats2raw/bioformats2raw-0.6.1/bin/bioformats2raw" aws_exec...

Any reason why this got moved to `Upload to BioStudies`? As per https://github.com/IDR/idr-metadata/issues/639#issuecomment-1587110746, I only remember converting a single plate and I thought the next step was to convert the...

For the full study conversion, I used the following script to generate the symlinks, the HTD file and commands to executed ```python import os sourcedir="/uod/idr/filesets/idr0035-caie-drugresponse/images" targetdir='/data/idr0035/sources/' zarrdir="/data/idr0035/zarr/" bf2raw_exec = "/opt/bioformats2raw/bioformats2raw-0.6.1/bin/bioformats2raw"...

``` (base) [sbesson@pilot-zarr1-dev zarr]$ ls Week10_40111.zarr Week1_22161.zarr Week2_24141.zarr Week3_25421.zarr Week3_25721.zarr Week4_27821.zarr Week5_29301.zarr Week6_31681.zarr Week7_34381.zarr Week8_38221.zarr Week9_39221.zarr Week10_40115.zarr Week1_22361.zarr Week2_24161.zarr Week3_25441.zarr Week4_27481.zarr Week4_27861.zarr Week5_29321.zarr Week6_32061.zarr Week7_34641.zarr Week8_38241.zarr Week9_39222.zarr Week10_40119.zarr Week1_22381.zarr Week2_24361.zarr...