From c19cdabd4dc56a6aa02737a60eb600c78d70a557 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 21 Jul 2021 10:02:55 +0300
Subject: Add some docs on how to edit data(probeset/ traits) from gn2

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 topics/gn1-migration-to-gn2/editing-data.gmi | 44 ++++++++++++++++++++++++++++
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 create mode 100644 topics/gn1-migration-to-gn2/editing-data.gmi

(limited to 'topics')

diff --git a/topics/gn1-migration-to-gn2/editing-data.gmi b/topics/gn1-migration-to-gn2/editing-data.gmi
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+### Introduction
+
+At the moment, you can edit metadata related to a published phenotype and a probeset. When an edit is done, the diff data is stored in a table, `metadata_audit` in json format that looks something like:
+
+```js
+{"Probeset": {"id_": {"old": "108845", "new": "108845"}, "description": {"old": "EST BG068973 (olfactory receptor related sequence).", "new": "EST BG068973 (olfactory receptor related sequence). Test"}}, "probeset_name": "1446112_at", "author": "Bonface Munyoki K.", "timestamp": "2021-07-10 08:31:18"}
+
+{"Probeset": {"id_": {"old": "108845", "new": "108845"}, "description": {"old": "EST BG068973 (olfactory receptor related sequence). Test", "new": "EST BG068973 (olfactory receptor related sequence). Testing"}}, "probeset_name": "1446112_at", "author": "Bonface Munyoki K.", "timestamp": "2021-07-10 08:31:36"}
+
+{"Probeset": {"id_": {"old": "108845", "new": "108845"}, "description": {"old": "EST BG068973 (olfactory receptor related sequence). Testing", "new": "EST BG068973 (olfactory receptor related sequence)."}}, "probeset_name": "1446112_at", "author": "Bonface Munyoki K.", "timestamp": "2021-07-10 10:15:37"}
+
+{"Phenotype": {"pre_pub_description": {"old": "Testing the description", "new": "Testing the description"}, "post_pub_description": {"old": "Central nervous system, morphology: Internal granule layer (IGL) of the cerebellum volume, adjusted for sex, age, body and brain weight [mm3]", "new": "Central nervous system, morphology: Internal granule layer (IGL) of the cerebellum volume, adjusted for sex, age, body and brain weight [mm3]"}, "original_description": {"old": "Original post publication description: Central nervous system, morphology: Internal granule layer (IGL) of the cerebellum volume, adjusted for sex, age, body and brain weight [mm3]", "new": "Original post publication description: Central nervous system, morphology: Internal granule layer (IGL) of the cerebellum volume, adjusted for sex, age, body and brain weight [mm3]"}, "units": {"old": "mm3", "new": "mm3"}, "pre_pub_abbreviation": {"old": "", "new": ""}, "post_pub_abbreviation": {"old": "AdjIGLVol", "new": "AdjIGLVol"}, "lab_code": {"old": "", "new": ""}, "submitter": {"old": "robwilliams", "new": "robwilliams"}, "owner": {"old": "", "new": ""}, "authorized_users": {"old": "robwilliams", "new": "robwilliams"}}, "dataset_id": "10007", "author": "Bonface Munyoki K.", "timestamp": "2021-07-16 16:35:56"}
+
+{"Phenotype": {"pre_pub_description": {"old": "Testing the description", "new": "Testing the descriptiony(test)"}}, "dataset_id": "10007", "author": "Bonface Munyoki K.", "timestamp": "2021-07-16 18:25:15"}
+```
+
+Note how we use one table to store different diffs from different data types. This is important, since if the need ever arises to use a different schema or db altogether, we only use one column.
+
+
+### Setup
+
+First, run [this](https://github.com/genenetwork/genenetwork3/blob/main/sql/metadata_audit.sql) sql script to add the "metadata<sub>audit</sub>" table.
+
+For everything to run, use the latest commit on the main branch from gn3. One way to make sure that you are running the latest changes, make sure that you have genenetwork3 cloned somewhere in your path; and keep it updated. Thereafter set, a PATH in "bin/genenetwork2" which should look something similar to `export PYTHONPATH=/home/bonface/projects/genenetwork3:$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$PYTHONPATH`.
+
+Alternatively, install gn3 in it's own profile. This can be sometimes inconvenient since the latest changes from gn3 can be ahead of the the package definition in our channel.
+
+
+### How to edit a trait Editing a trait/ probeset
+
+These are the steps you can do to edit a phenotype/ probeset:
+
+-   Log in to a trait page or a probeset (Make sure that your are logged in). From the "Trait Data and Analysis page" for the probeset/ trait, there's an "Edit" button under "Details and Links". Use this to edit the metadata.
+
+-   An example of editing a published phenotype is: "*trait/10007/edit/inbredset-id/10007*"
+
+After editing traits, you could see changes in a diff format at the very top of the update page.
+
+
+### Notes
+
+-   Atm, creds are hard-coded. See: <https://github.com/genenetwork/genenetwork2/blob/testing/wqflask/wqflask/decorators.py>. That needs to be improved.
+
+-   For Probeset data, atm some tables aren't yet updated(unfortunately those tables aren't used anywhere). I need to figure that out.
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