diff --git a/doc/source/_static/fex-email.png b/doc/source/_static/fex-email.png new file mode 100644 index 0000000000000000000000000000000000000000..805895633e15354a90ded616656e7f2a1f05245a Binary files /dev/null and b/doc/source/_static/fex-email.png differ diff --git a/doc/source/_static/fex-upload.png b/doc/source/_static/fex-upload.png new file mode 100644 index 0000000000000000000000000000000000000000..0ebe5de3ba7efa84de7acb7053106a13b9f9dbff Binary files /dev/null and b/doc/source/_static/fex-upload.png differ diff --git a/doc/source/_static/gitlab-pipelines-delete-file.png b/doc/source/_static/gitlab-pipelines-delete-file.png new file mode 100644 index 0000000000000000000000000000000000000000..5755883efd524bf88773d7fc489195555cc42af4 Binary files /dev/null and b/doc/source/_static/gitlab-pipelines-delete-file.png differ diff --git a/doc/source/_static/gitlab-pipelines.png b/doc/source/_static/gitlab-pipelines.png new file mode 100644 index 0000000000000000000000000000000000000000..d937f929185d1ec8cb6700c5f4c042268e43e67c Binary files /dev/null and b/doc/source/_static/gitlab-pipelines.png differ diff --git a/doc/source/_static/job-done-with-filename.png b/doc/source/_static/job-done-with-filename.png new file mode 100644 index 0000000000000000000000000000000000000000..d5995d05c964c09d25f535073f96f65e997e470c Binary files /dev/null and b/doc/source/_static/job-done-with-filename.png differ diff --git a/doc/source/_static/job-done-with-url.png b/doc/source/_static/job-done-with-url.png new file mode 100644 index 0000000000000000000000000000000000000000..a980c320c29bd02455009b905a41dc0f4e96d29f Binary files /dev/null and b/doc/source/_static/job-done-with-url.png differ diff --git a/doc/source/_static/trigger-job-with-filename.png b/doc/source/_static/trigger-job-with-filename.png new file mode 100644 index 0000000000000000000000000000000000000000..cd5d4c9eb4cbed8892a5594589d18d23787dd022 Binary files /dev/null and b/doc/source/_static/trigger-job-with-filename.png differ diff --git a/doc/source/_static/trigger-job-with-url.png b/doc/source/_static/trigger-job-with-url.png new file mode 100644 index 0000000000000000000000000000000000000000..a7e87b80eb4ae58e5dc467a1cdcc99a8b41fa4b0 Binary files /dev/null and b/doc/source/_static/trigger-job-with-url.png differ diff --git a/doc/source/index.rst b/doc/source/index.rst index d49fff3e7ccac801b7973a949298e7ee1d3fa107..270f8c072ce9a715e642250b4daf5aa1b29772b3 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -16,6 +16,7 @@ JASS documentation generating_joint_analysis command_line_usage web_usage + web_admin develop Indices and tables diff --git a/doc/source/web_admin.rst b/doc/source/web_admin.rst new file mode 100644 index 0000000000000000000000000000000000000000..f2acb5df80c57487be9bb87b00fc1d40efee8221 --- /dev/null +++ b/doc/source/web_admin.rst @@ -0,0 +1,86 @@ +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% \ No newline at end of file