installation error

[ziltonvasconcelos]

when running the last step of installation:

uv run scout

I received this error below....can anyone help?

Thanks a lot!

root@vm-applications:/home/zvasconcelos/scout# uv run scout
Traceback (most recent call last):
  File "/home/zvasconcelos/scout/.venv/bin/scout", line 5, in <module>
    from scout.commands import cli
  File "/home/zvasconcelos/scout/scout/commands/__init__.py", line 1, in <module>
    from .base import cli
  File "/home/zvasconcelos/scout/scout/commands/base.py", line 26, in <module>
    from scout.server.app import create_app
  File "/home/zvasconcelos/scout/scout/server/app.py", line 19, in <module>
    from .blueprints import (
  File "/home/zvasconcelos/scout/scout/server/blueprints/cases/__init__.py", line 2, in <module>
    from .views import cases_bp
  File "/home/zvasconcelos/scout/scout/server/blueprints/cases/views.py", line 13, in <module>
    from cairosvg import svg2png
  File "/home/zvasconcelos/scout/.venv/lib/python3.12/site-packages/cairosvg/__init__.py", line 26, in <module>
    from . import surface  # noqa isort:skip
    ^^^^^^^^^^^^^^^^^^^^^
  File "/home/zvasconcelos/scout/.venv/lib/python3.12/site-packages/cairosvg/surface.py", line 9, in <module>
    import cairocffi as cairo
  File "/home/zvasconcelos/scout/.venv/lib/python3.12/site-packages/cairocffi/__init__.py", line 60, in <module>
    cairo = dlopen(
            ^^^^^^^
  File "/home/zvasconcelos/scout/.venv/lib/python3.12/site-packages/cairocffi/__init__.py", line 57, in dlopen
    raise OSError(error_message)  # pragma: no cover
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: no library called "cairo-2" was found
no library called "cairo" was found
no library called "libcairo-2" was found
cannot load library 'libcairo.so.2': libcairo.so.2: cannot open shared object file: No such file or directory.  Additionally, ctypes.util.find_library() did not manage to locate a library called 'libcairo.so.2'
cannot load library 'libcairo.2.dylib': libcairo.2.dylib: cannot open shared object file: No such file or directory.  Additionally, ctypes.util.find_library() did not manage to locate a library called 'libcairo.2.dylib'
cannot load library 'libcairo-2.dll': libcairo-2.dll: cannot open shared object file: No such file or directory.  Additionally, ctypes.util.find_library() did not manage to locate a library called 'libcairo-2.dll'

[dnil]

Hi there! Happy new year! Very glad to see you are using Scout and the new install option! The same as before applies though, that for the sake of reports you will need to have some pdf generation libraries installed on your os - see the next couple of paragraphs on the installation page (quoted below). The installation procedure for these differ according to your OS. You can also consider running with Docker which will preinstall them in the image and you don't have to worry what is on your system! 😊

Scout PDF reports are created using Flask-WeasyPrint. This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation pages.

NB: in order to convert HTML reports into PDF reports, we have recently switched from the WeasyPrint lib to python-pdfkit. For this reason, when upgrading to a Scout version >4.47, you need to install an additional wkhtmltopdf system library.

[ziltonvasconcelos]

I am happy to say that I´ve updated my python version to 3.9 and everything seems to work and I received the output below

root@vm-applications:/home/zvasconcelos/scout# uv run scout 2025-01-10 00:06:44 vm-applications scout.commands.base[101744] INFO Running scout version 4.94.1 2025-01-10 00:06:44 vm-applications scout.adapter.client[101744] INFO Connected to MongoDB 8.0.4 2025-01-10 00:06:44 vm-applications scout.adapter.mongo.base[101744] INFO Database name: scout 2025-01-10 00:06:44 vm-applications scout.server.app[101744] INFO Enable Phenopacket API
But then I´ve tried to connect to localhost:8000 and no way to reach the software....Am I missing something?

[northwestwitch]

I am happy to say that I´ve updated my python version to 3.9 and everything seems to work and I received the output below

root@vm-applications:/home/zvasconcelos/scout# uv run scout 2025-01-10 00:06:44 vm-applications scout.commands.base[101744] INFO Running scout version 4.94.1 2025-01-10 00:06:44 vm-applications scout.adapter.client[101744] INFO Connected to MongoDB 8.0.4 2025-01-10 00:06:44 vm-applications scout.adapter.mongo.base[101744] INFO Database name: scout 2025-01-10 00:06:44 vm-applications scout.server.app[101744] INFO Enable Phenopacket API But then I´ve tried to connect to localhost:8000 and no way to reach the software....Am I missing something?

Nice!

Try instead uv run scout --demo serve
Then if you go to the browser (localhost:5000) you should be able to see the interface! 🤞🏻

If this doesn't work it might be because you don't have a MongoDB instance running.

[dnil]

Super! Good to hear. At some point, you will want to migrate to later python for production, but for testing 3.9 should be all good. With uv, updating python is supposedly really easy. 😁
As @northwestwitch writes, uv run scout --demo serve will fire up a simple test web server. Did you successfully run uv run scout setup demo already? That will populate your db with demo data so you have something to look at.
Then when you feel ready you can go on to scout setup database and go through the full loading of data, starting with a scout download everything --api-key your_hard_earned_omim_api_key etc.

For production, you will want to serve the app through the likes of gunicorn or another production grade server. See documentation, and shout if it is incomplete somewhere! 😸

[ziltonvasconcelos]

I cannot connect to localhost...this is what I see in the server:

`root@vm-applications:/home/zvasconcelos/scout# uv run scout --demo serve
2025-01-10 22:53:27 vm-applications scout.commands.base[105825] INFO Running scout version 4.94.1
2025-01-10 22:53:27 vm-applications scout.adapter.client[105825] INFO Connected to MongoDB 8.0.4
2025-01-10 22:53:27 vm-applications scout.adapter.mongo.base[105825] INFO Database name: scout-demo
2025-01-10 22:53:27 vm-applications scout.server.app[105825] INFO Enable Phenopacket API
DeprecationWarning: The command 'serve' is deprecated.
2025-01-10 22:53:27 vm-applications werkzeug[105825] INFO WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.

• Running on http://localhost:5000
  2025-01-10 22:53:27 vm-applications werkzeug[105825] INFO Press CTRL+C to quit
  `

And this is what I receive in the browser:

[dnil]

Nicely done! I don't think this is a Scout issue any more really - if you see that text I'm very sure Scout is running and serving on localhost:5000.

This is going slightly into trying to help with your network settings without knowing your setup, but from the looks of it you are trying to connect to your machines external interface IP? Is it possible that you have some routing or filter between that and your internal one? Or is it some sort of virtual machine that needs a bit of port opening for this to work?

If it is bare metal you should just be able to point your browser to localhost:5000 or like 192.168.0.1:5000 or whatever your local interface is. Just be conscious of the difference in routing and you should find it just fine!

You can always check from the command line with like 'curl' or 'wget' from localhost:5000 to convince yourself it is serving the scout html.