lambda-science / impatient Goto Github PK

Backlog of ideas to improve the dashboard module:

• Don't re-do all calculations and viz when visiting the page, only trigger it on ontology change or new reports.

Delete legacy code, config files and text that will not be use for publication.

Backlog of ideas to improve the vocabulary module:

• Switch lang button should become FRA/ENG buttons (two sepearates buttons), might use JSTree metadata field to check the current vocab language
• Add a "image annotation" tickbox as nodes properties (boolean) to show or not on image annotation module

Backlog of ideas to for META improvement (structure, deployment...):

• Add Admin Interface to create accounts
• Remove NGINX Cache or try with production settings (to fix images issues ?)
• Might add a role-base / user-based gestion of data

Modify Show Segmentation to Button
Modify Blurring parameters to a single value
Modify tag list to Standard vocabulary part "image tagging"
If classifier is not none load it

All input in database should be encrypted using AES-256 bits.

1. Set the secret key in the .env file
2. Make sure all form encrypt data before saving to DB.
3. Use secret key to read data

Reference:

• Generate key: https://www.allkeysgenerator.com/Random/Security-Encryption-Key-Generator.aspx
• CBC Algo with IV patient: https://python-guide-pt-br.readthedocs.io/fr/latest/scenarios/crypto.html

• Download table as CSV
• Automatic Graph by age / diag / muscle
• Automatic correlation Matrix

Add title, axis colors to plots.
Add BOQA Results ?

Title.

Would probably be better to migrate to a conda env for more cross-platform compatibility.

no distinction gene / gene datamined
sort genes
show un-asigned genes
find complete gene list
synonymes + other lang

Also load CLF and trigger the classif

Backlog of ideas to improve the image module:

• Find out why sometimes annotations don't show up on refresh, same question for image
• Find out why the layout doesn't get updated when new terms are added (remove cache ?)
• Fix the form image upload issue when modifying data (New Form ?)
• Load previous model for new images ?
• Simplify code base

Add BOQA Results and UNCLEAR reclassification.
For each report store prediction in DB so not always calculated

Clicking on Image Annotation Link when not being on the root URL is bugged.

Per trms genes: show all and marks linked as colored
Changer info terms de champs à HTML classique
Ajouter champs gene suspecté, modifier diagnosed as tag list

A Security Advisory has been raised for IMPatienT v1.5.0 (CVE-2023-23637):

Description:
IMPatienT v1.5.0 allows Stored Cross-Site Scripting (XSS) via onmouseover in certain text fields within a PATCH /modify_onto request.
This may allow attackers to steal Protected Health Information (PHI).

Suggested Fix:
Consider sanitizing user input parameters by removing all non-compliant characters. Additionally, you could consider encoding the user input using HTML or URL methods.

Reference:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2023-23637
https://nvd.nist.gov/vuln/detail/CVE-2023-23637
https://owasp.org/www-project-top-ten/2017/A7_2017-Cross-Site_Scripting_(XSS)

Payload:

PATCH /modify_onto HTTP/1.1
Host: 127.0.0.1:5000
Content-Length: 2218
Content-Type: application/x-www-form-urlencoded; charset=UTF-8
User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/109.0.5414.75 Safari/537.36
Origin: http://127.0.0.1:5000/
Referer: http://127.0.0.1:5000/ontocreate
Connection: close

[{"id":"MHO:000001","text":"Sample Keyword","icon":true,"li_attr":{"id":"MHO:000001"},"a_attr":{"href":"#","id":"MHO:000001_anchor"},"state":{"loaded":true,"opened":true,"selected":false,"disabled":false},"data":{"description":"","synonymes":"","phenotype_datamined":"","gene_datamined":"","alternative_language":"Sample Keyword","hex_color":"#c7ef34","hpo_datamined":"","correlates_with":"","image_annotation":false},"parent":"#"},{"id":"MHO:000004","text":"Keyword Image Annotation","icon":true,"li_attr":{"id":"MHO:000004"},"a_attr":{"href":"#","id":"MHO:000004_anchor"},"state":{"loaded":true,"opened":false,"selected":true,"disabled":false},"data":{"description":"","synonymes":"","phenotype_datamined":"UNCLEAR","gene_datamined":"N/A","alternative_language":"","correlates_with":"","image_annotation":true,"hex_color":"#77e3a4","hpo_datamined":""},"parent":"MHO:000001"},{"id":"MHO:000005","text":"Keyword Image Annotation 2<a onmouseover=alert('XSS')>XSS</a>","icon":true,"li_attr":{"id":"MHO:000005"},"a_attr":{"href":"#","id":"MHO:000005_anchor"},"state":{"loaded":true,"opened":false,"selected":false,"disabled":false},"data":{"description":"","synonymes":"","phenotype_datamined":"","gene_datamined":"","alternative_language":"","correlates_with":"","image_annotation":true,"hex_color":"#094f6a","hpo_datamined":""},"parent":"MHO:000001"},{"id":"MHO:000002","text":"Sample Keyword Child","icon":true,"li_attr":{"id":"MHO:000002"},"a_attr":{"href":"#","id":"MHO:000002_anchor"},"state":{"loaded":true,"opened":false,"selected":false,"disabled":false},"data":{"description":"","synonymes":"","phenotype_datamined":"","gene_datamined":"","alternative_language":"","correlates_with":"","image_annotation":false,"hex_color":"#14cd17","hpo_datamined":""},"parent":"MHO:000001"},{"id":"MHO:000003","text":"Sample Keyword Child 2","icon":true,"li_attr":{"id":"MHO:000003"},"a_attr":{"href":"#","id":"MHO:000003_anchor"},"state":{"loaded":true,"opened":false,"selected":false,"disabled":false},"data":{"description":"","synonymes":"","phenotype_datamined":"","gene_datamined":"","alternative_language":"","correlates_with":"","image_annotation":false,"hex_color":"#d9eab9","hpo_datamined":""},"parent":"MHO:000001"}]

Backlog of ideas to improve the report module:

• Add a red X button to vocabulary terms overview
• Add RegEx to prefill age, biopsy ID and date
• Hide the debug modal
• Add a modified patient hook in SQLite DB to redo visualisations automatically (and not always)

Title

Check all translation in code, pages and ontology to prepare for publication

• Mutation Field + Phenotype field
• Re-use model for image
• Tiff file convertion

Find a way in the image annotation module to upload an image, select the image from DB and save/load the annotations.
One possible way would be a separate page for image uploading.