20.01 + python3, error starting reports webapp

[abretaud]

Hi,
I made a quick test on my dev server to update to 20.01 + switch to python3. I removed .venv, and at startup it successfully created the galaxy conda env, and the new .venv virtualenv. But I get this error when starting the report webapp:

galaxy.webapps.util DEBUG 2020-02-28 17:32:40,532 [p:6566,w:0,m:0] [MainThread] Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2020-02-28 17:32:40,534 [p:6566,w:0,m:0] [MainThread] Enabling 'RecursiveMiddleware' middleware
galaxy.webapps.util DEBUG 2020-02-28 17:32:40,549 [p:6566,w:0,m:0] [MainThread] Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2020-02-28 17:32:40,551 [p:6566,w:0,m:0] [MainThread] Enabling 'TransLogger' middleware
galaxy.webapps.util DEBUG 2020-02-28 17:32:40,554 [p:6566,w:0,m:0] [MainThread] Enabling 'XForwardedHostMiddleware' middleware
galaxy.webapps.util WARNING 2020-02-28 17:32:40,554 [p:6566,w:0,m:0] [MainThread] 'wrap_in_static' is enabled in your configuration but the uWSGI application stack does not support it, this middleware has been disabled
WSGI app 0 (mountpoint='') ready in 5 seconds on interpreter 0x55c8f8e960d0 pid: 6566 (default app)
mounting galaxy.webapps.reports.buildapp:uwsgi_app() on /reports
added lib/ to pythonpath.
Traceback (most recent call last):
  File "lib/galaxy/webapps/reports/buildapp.py", line 12, in <module>
    import galaxy.model.mapping
  File "lib/galaxy/model/mapping.py", line 41, in <module>
    from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
  File "lib/galaxy/model/custom_types.py", line 10, in <module>
    import numpy
  File "/opt/galaxy_dev/galaxy-dist/.venv/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/opt/galaxy_dev/galaxy-dist/.venv/lib/python3.6/site-packages/numpy/core/__init__.py", line 40, in <module>
    from . import multiarray
  File "/opt/galaxy_dev/galaxy-dist/.venv/lib/python3.6/site-packages/numpy/core/multiarray.py", line 13, in <module>
    from . import overrides
  File "/opt/galaxy_dev/galaxy-dist/.venv/lib/python3.6/site-packages/numpy/core/overrides.py", line 46, in <module>
    """)
RuntimeError: implement_array_function method already has a docstring
unable to load app 1 (mountpoint='/reports') (callable not found or import error)
*** daemonizing uWSGI ***

No error when starting galaxy though

[mvdbeek]

Hmm, that looks like a dependency issue. Can you check what version of numpy this is, and maybe re-install it ?

[abretaud]

Strange, numpy==1.16.5 is installed in the venv, the same as in requirements.txt.
I tried uninstalling/reinstalling, but still the same problem

[mvdbeek]

Looks like numpy/numpy#14384 :/

[abretaud]

Arf, looks complicated
I'm surprised that I only get it with reports and not galaxy itself

[mvdbeek]

surprisingly it works fine for me with uwsgi and python 3.6 -- but there's is a linked commit that suggests that 1.15.4 works. Could you try that ?

[abretaud]

So, using 1.15.4, I get another error:

galaxy.webapps.util DEBUG 2020-03-02 11:33:46,438 [p:6620,w:0,m:0] [MainThread] Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2020-03-02 11:33:46,440 [p:6620,w:0,m:0] [MainThread] Enabling 'RecursiveMiddleware' middleware
galaxy.webapps.util DEBUG 2020-03-02 11:33:46,448 [p:6620,w:0,m:0] [MainThread] Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2020-03-02 11:33:46,449 [p:6620,w:0,m:0] [MainThread] Enabling 'TransLogger' middleware
galaxy.webapps.util DEBUG 2020-03-02 11:33:46,450 [p:6620,w:0,m:0] [MainThread] Enabling 'XForwardedHostMiddleware' middleware
galaxy.webapps.util WARNING 2020-03-02 11:33:46,450 [p:6620,w:0,m:0] [MainThread] 'wrap_in_static' is enabled in your configuration but the uWSGI application stack does not support it, this middleware has been disabled
WSGI app 0 (mountpoint='') ready in 4 seconds on interpreter 0x55ff90c4c0d0 pid: 6620 (default app)
mounting galaxy.webapps.reports.buildapp:uwsgi_app() on /reports
added lib/ to pythonpath.
Traceback (most recent call last):
  File "lib/galaxy/webapps/reports/buildapp.py", line 135, in uwsgi_app
    return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "reports")
  File "lib/galaxy/web/framework/webapp.py", line 995, in build_native_uwsgi_app
    uwsgi_app = paste_factory({}, load_app_kwds=app_kwds)
  File "lib/galaxy/webapps/reports/buildapp.py", line 62, in app_factory
    add_ui_controllers(webapp, app)
  File "lib/galaxy/webapps/reports/buildapp.py", line 30, in add_ui_controllers
    from galaxy.webapps.base.controller import BaseUIController
  File "lib/galaxy/webapps/base/controller.py", line 21, in <module>
    from galaxy.datatypes.interval import ChromatinInteractions
  File "lib/galaxy/datatypes/interval.py", line 9, in <module>
    from bx.intervals.io import GenomicIntervalReader, ParseError
  File "/opt/galaxy_dev/galaxy-dist/.venv/lib/python3.6/site-packages/bx/intervals/__init__.py", line 7, in <module>
    from bx.intervals.intersection import *  # noqa: F40
ImportError: Interpreter change detected - this module can only be loaded into one interpreter per process.
unable to load app 1 (mountpoint='/reports') (callable not found or import error)
*** daemonizing uWSGI **

I got it running by switching back to 1.16.5 and adding this to reports.yml:

  single-interpreter: true

[martenson]

this is likely resolved or outdated