bcgsc / pori

Platform for Oncogenomic Reporting and Interpretation (PORI)

Platform for Oncogenomic Reporting and Interpretation (PORI)

The Platform for Oncogenomic Reporting and Interpretation (PORI) is an open source collection of software designed to support scaleable precision oncology. The platform has two main components: a graph knowledge base (GraphKB) and an integrated pipeline reporting application (IPR).

For more information see the related user manual

Demo

A live demo of this is found at: pori-demo.bcgsc.ca. This demo was deployed via docker-compose

Citation

Please cite Reisle, C. et al. A platform for oncogenomic reporting and interpretation. Nat. Commun. 13, 1–11 (2022)

Building the Docs (Developers)

The main PORI site is built from this repo and pull documentation files from the python adapter repos. The documentation is built using mkdocs. The main website will be updated on merge to the master branch of this repository.

First, set up a virtual environment (Optional but recommended)

python3 -m venv venv
source venv/bin/activate
pip install -U setuptools pip

Install the python dependencies

pip install -r requirements.txt

Run the script to pull the other respository files

bash docs/build_external.sh

And finally serve the documentation for viewing locally with

mkdocs serve

pori's Issues

requests.exceptions.HTTPError: 401 Client Error

Hello, I installed PORI docker stack for local machine. When I tried to upload a demo report, I got the error below. I noticed that even I provided a URL, ipr didn't use it and uses https://graphkb-api.bcgsc.ca/api/token not local address. OS is centos 7, RAM 8GB, disk 20gb space, browser firefox 91.7, docker v20. How can I solve this problem?

(ipr_stable) [aliriza@localhost Desktop]$ ipr -c demo_report.json --ipr_url http://127.0.0.1:8081/api --username iprdemo --password iprdemo
Traceback (most recent call last):
  File "/home/aliriza/miniconda3/envs/ipr_stable/bin/ipr", line 8, in <module>
    sys.exit(command_interface())
  File "/home/aliriza/miniconda3/envs/ipr_stable/lib/python3.8/site-packages/ipr/main.py", line 87, in command_interface
    create_report(
  File "/home/aliriza/miniconda3/envs/ipr_stable/lib/python3.8/site-packages/ipr/main.py", line 185, in create_report
    graphkb_conn.login(username, password)
  File "/home/aliriza/miniconda3/envs/ipr_stable/lib/python3.8/site-packages/graphkb/__init__.py", line 137, in login
    resp.raise_for_status()
  File "/home/aliriza/miniconda3/envs/ipr_stable/lib/python3.8/site-packages/requests/models.py", line 960, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 401 Client Error: Unauthorized for url: https://graphkb-api.bcgsc.ca/api/token

docker images are working fine:

Thanks.

Error on the example script

Hi,

In this tutorial code, get_sample_by_name is not defined. Can you tell me where I get this function?

pori/docs/graphkb/scripting/Annotate_a_VCF_with_GraphKB.ipynb

Line 439 in df616ca

" tumour_sample = get_sample_by_name(record, 'TUMOR')\n",

Add mini report upload test to compose start test

Add a step to attempt uploading a report as part of the main compose up tests. Should be added after the script that is called here

https://github.com/bcgsc/pori/blob/master/.github/workflows/compose-test.yml#L15

Use the simplest possible report (no variants) to avoid having a long-running test

ports defined in docker-composer.dev.yml

Hello, I need to clarify the ports defined in docker-composer.dev.yml. Are these ports correct?

Update pori docs to include comparator ('analysis role') name definitions

Update the docs to accompany the added comparator type 'internal pancancer': https://bcgsc.github.io/pori/ipr/core_variants/expression/#comparators

Perhaps we can add an exhaustive list of definitions for each of the comparators here: https://bcgsc.github.io/pori/ipr/optional_analyses/comparators/

(paraphrased from linked comment by @creisle)

Originally posted by @creisle in bcgsc/pori_ipr_python#82 (comment)

request pending from IPR client to API in dev docker setup

When I updated to the latest images for some reason the requests seem to hang and not complete (see GIF below)

https://github.com/bcgsc/pori/blob/master/.github/workflows/compose-test.yml#L15

I am testing this off dev branch here currently: https://github.com/bcgsc/pori/tree/feature/re-install-instructions

@kttkjl or @brayden-bcgsc or @mathieulemieux have any of you run into this? Did the CORS permissions change at all in the latest releases?

Invalid parameter: redirect_uri

Describe the bug
When accessing graphkb_client latest version, page redirects(to this link) and show an error. 10.100.120.219 is our server internal ip address.

Invalid parameter: redirect_uri

I wanted to put graphkb(latest) on production.

To Reproduce
Steps to reproduce the behaviour:

1. Run command docker-compose -f custom_docker.yml up -d
2. Access grapkb_client at http://10.100.120.219:5000/
3. Page shows error

here is my custom_docker.yml:
custom_docker.txt

Expected behaviour
Graphkb login screen should be visible.

Versions (please complete the following information):

• OS: centos 7
• NodeJS: 16.14.2
• Version: latest
• OrientDB Version: 3.0

Additional context
I don't use HTTPS. My first aim is to run PORI without any error. Then I hope to use HTTPS.

update pori demo link destination

Copied from comment by @mathieulemieux :

While reviewing pori demo docs, I saw these two links:

• pori/docs/demo.md

  Line 3 in df616ca

  A live demo of the platform is found under `pori-demo.bcgsc.ca`. This demo was deployed via docker-compose.

• pori/docs/graphkb/index.md

  Line 51 in df616ca

  The simplest way to try out GraphKB is via the demo we provide [here](https://pori-demo.bcgsc.ca/).

  
  from which we are being redirected to the docs on GH and find it a bit confusing. What about removing them or changing them for the /ipr and /graphkb routes?

Originally posted by @mathieulemieux in #59 (comment)

Update docker-compose files for database schema

Docker-compose needs to be updated as it is not using an up-to-date database schema, as per comment #51 (comment).

Make shared default admin demo user for GraphKB/IPR

To simplify the setup it would be great to add the same admin user for both IPR and GraphKB. This will require the following tasks

• @mathieulemieux to change the default "graphkb_admin" user in the graphkb api repo to be "pori_admin"
• @brayden-bcgsc to add a new "pori_admin" user to the IPR default db dump with admin access to IPR
• @mathieulemieux or @brayden-bcgsc to rename the user "graphkb_admin" in the keycloak dump json to pori_admin and update the accompanying docs