Import metadata using the Command Line Interface (CLI)¶
This chapter will show how to import metadata starting from a local CSV file and ending with OMERO.tables on images or Key-Value pairs on images using the Command Line Interface (CLI). For a more user-friendly way of uploading metadata using graphical interface see the Import metadata using the Populate Metadata script in OMERO.web chapter.
This action is typically done after a successful import of images.
We will show:
- How to import metadata from local CSV file in a bulk manner and turn them into OMERO.tables on images using CLI
- How to turn the OMERO.tables on images into Key-Value pairs on images in bulk manner using CLI
- How to import metadata from local CSV file and use a server-side script in OMERO to turn these into OMERO.tables on images
- How to construct a simple file to turn the metadata stored in OMERO.tables into Key-Value pairs on images using CLI
- Data: example images from
- Metadata plugin for OMERO
- Bulkmap config yml files defining the various Key-Value pairs parameters, such as the groups and other parameters.
- Annotation CSV files define the content of OMERO.tables for each image.
Metadata plugin installation
Go to the environment where you installed your OMERO.cli as specified under - CLI installation.
Activate the virtual environment.
$ pip install omero-metadata
On your local machine, open a terminal
If you did not do so already, activate the virtual environment where
omero-pyis installed or add it to
$ export PATH=/opt/omero/server/venv3/bin:$PATH
Download the CSV from idr0021-experimentA-annotation.csv if you have access to the idr0021 data in your OMERO.server. Alternatively, download
simple-annotation.csv, which will allow you to work with the siRNAi-HeLa dataset.
$IDbelow is the ID of the Project, in this example case it is the Project containing the idr0021 study. If you are working with the siRNAi-HeLa data, replace in the following example the “Project” with a “Dataset” and the
simple-annotation.csv. To add annotations from a local CSV file to the images in the said Project or Dataset in the form of OMERO.tables, run:
$ omero metadata populate --report --batch 1000 --file local/path/to/idr0021-experimentA-annotation.csv Project:$ID
Open your browser and login to the OMERO.web. Navigate to the Project or Dataset you just worked with, expand the “Attachments” harmonica in the right-hand pane and verify that a new attachment is on that Project named
Select an image inside the Project/Dataset and expand the “Tables” harmonica in the right-hand pane. These tables contain the appropriate line from the
bulk_annotationsattachment you just created for that particular image.
Go back to your terminal. Download the idr0021-experimentA-bulkmap-config.yml file . Alternatively, in case you are working with the siRNAi-HeLa Dataset, download
If you are working with the IDR data, open the downloaded
idr0021-experimentA-bulkmap-config.ymlfile in a text editor and delete the
Advanced options...section. Save the file and run:
$ omero metadata populate --context bulkmap --cfg local/path/to/idr0021-experimentA-bulkmap-config.yml --batch 100 Project:$ID
If you work with the siRNAi-HeLa data, open the downloaded
simple-annotation-bulkmap-config.ymland study the comments in the file itself, which will give you hints about how to manipulate the file to fit your particular needs with respect to the resulting Key-Value pairs layout. Make your changes (no need to change anything if you do not want), save the file locally and run:
$ omero metadata populate --context bulkmap --cfg local/path/to/simple-annotation-bulkmap-config.yml --batch 100 Dataset:$ID
Go to your browser and in OMERO.web, select the images in the Project or Dataset you targeted and verify that they have now new Key-Value pairs displayed in the right-hand pane.