From 29d3b23e48bac18b60a11728ac3f72ec11f41ca2 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 12 Jun 2020 15:34:05 +0100 Subject: [PATCH] review link display --- docs/metadata.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/metadata.rst b/docs/metadata.rst index 808ad01..0f65b57 100644 --- a/docs/metadata.rst +++ b/docs/metadata.rst @@ -23,14 +23,14 @@ Resources - Documentation: - - https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html + - `CLI installation `_ - - `https://docs.openmicroscopy.org/omero/latest/users/cli/index.html `__ + - `CLI `__ - Data: example images from - - IDR data https://idr.openmicroscopy.org/webclient/?show=project-51 - - siRNAi-HeLa dataset from https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/ + - IDR data `idr0021-lawo-pericentriolarmaterial/experimentA `_ + - `siRNAi-HeLa `_ dataset - Metadata plugin for OMERO @@ -38,12 +38,12 @@ Resources - Bulkmap config yml files defining the various Key-Value pairs parameters, such as the groups and other parameters. - - https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-bulkmap-config.yml + - `idr0021-experimentA-bulkmap-config.yml `_ - :download:`simple-annotation-bulkmap-config.yml <../scripts/simple-annotation-bulkmap-config.yml>` - Annotation CSV files define the content of OMERO.tables for each image. - - https://github.com/IDR/idr0021-lawo-pericentriolarmaterial/blob/9479af85f19487f215e3dfdd31a1b587370ed3cf/experimentA/idr0021-experimentA-annotation.csv + - `idr0021-experimentA-annotation.csv `_ - :download:`simple-annotation.csv <../scripts/simple-annotation.csv>` - :download:`four-images.csv <../scripts/four-images.csv>` @@ -52,7 +52,7 @@ Setup **Metadata plugin installation** -- Go to the environment where you installed your OMERO.cli as specified under - https://docs.openmicroscopy.org/omero/latest/users/cli/installation.html. +- Go to the environment where you installed your OMERO.cli as specified under - `CLI installation `_. - Activate the virtual environment. @@ -69,7 +69,7 @@ Step-by-step $ export PATH=/opt/omero/server/venv3/bin:$PATH -#. Download the CSV from `idr0021-experimentA-annotation.csv `_ if you have access to the `idr0021 `_ data in your OMERO.server. Alternatively, download :download:`simple-annotation.csv <../scripts/simple-annotation.csv>`, which will allow you to work with the siRNAi-HeLa dataset, which you can download from https://downloads.openmicroscopy.org/images/DV/siRNAi-HeLa/. +#. Download the CSV from `idr0021-experimentA-annotation.csv `_ if you have access to the `idr0021 `_ data in your OMERO.server. Alternatively, download :download:`simple-annotation.csv <../scripts/simple-annotation.csv>`, which will allow you to work with the `siRNAi-HeLa `_ dataset. #. The variable ``$ID​`` below 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 ``idr0021-experimentA-annotation.csv`` with ``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::