document upload procedure

doc/source/index.rst

@@ -16,6 +16,7 @@ JASS documentation
    generating_joint_analysis
    command_line_usage
    web_usage
+   web_admin
    develop
 
 Indices and tables

doc/source/web_admin.rst

+Web admin
+===============================================================================
+
+Updating data
+-------------------------------------------------------------------------------
+
+You can update data using kubectl, to do so see this `"How To" <https://gitlab.pasteur.fr/statistical-genetics/jass/-/blob/master/chart/HOWTO.md?ref_type=heads#updating-data-including-inittablehdf5>`_.
+
+An alternative using fex.pasteur.fr is also proposed, with no binary to install locally.
+
+Upload to fex
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Go to https://fex.pasteur.fr/fup, click on "fex yourself" and choose the file you want to send.
+In our example it is initTableTest.hdf5
+
+.. image:: _static/fex-upload.png
+  :width: 100%
+
+Get the fex link
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You then receive an email containing the url where the initTable is available, copy it.
+In our example it is https://dl.pasteur.fr/fop/6atgurR3/initTableTest.hdf5
+
+.. image:: _static/fex-email.png
+  :width: 100%
+
+Go to gitlab pipelines
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Go to https://gitlab.pasteur.fr/statistical-genetics/jass/-/pipelines
+
+Click on the last grey/green circle on the right (indicated 1 in the following image).
+Then on the task ``upload-from-fex-to-dev`` (indicated 2) if you want to send the file in dev.
+A job is also proposed related to master pipelines.
+
+.. image:: _static/gitlab-pipelines.png
+  :width: 100%
+
+Trigger while providing the URL
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Provide in an variable name ``FEX_URL`` the url.
+In our example ``FEX_URL=https://dl.pasteur.fr/fop/6atgurR3/initTableTest.hdf5``
+
+.. image:: _static/trigger-job-with-url.png
+  :width: 100%
+
+After some time the job is completed, you see with the ls that the file is now there.
+
+After the job is completed, in the right part you see "Job artifact", when browsing them you have the
+file you have added, and the previous one that was replaced.
+Artefact are keep 1 month as of March 2024.
+
+.. image:: _static/job-done-with-url.png
+  :width: 100%
+
+Deleting data
+-------------------------------------------------------------------------------
+
+You can also simply delete hdf5 file (and only them).
+
+Go to https://gitlab.pasteur.fr/statistical-genetics/jass/-/pipelines
+
+Click on the last grey/green circle on the right (indicated 1 in the following image).
+Then on the task ``delete-data-from-dev`` (indicated 2).
+
+.. image:: _static/gitlab-pipelines-delete-file.png
+  :width: 100%
+
+Trigger while providing the filename
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Provide in an variable name ``HDF5_FILENAME`` the hdf5 filename (no relative path allowed).
+In our example ``HDF5_FILENAME=initTableTest.hdf5``
+
+.. image:: _static/trigger-job-with-filename.png
+  :width: 100%
+
+Also in the right part you see "Job artifact", when browsing them you have the
+file you just removed.
+Artefact are keep 1 month as of March 2024.
+
+.. image:: _static/job-done-with-filename.png
+  :width: 100%
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