ot_ws_wrapper NoneType

[mkandziora]

command:
physcraper_run.py -s ot_350 -t Tr53297 -tb -db PATH_TO_LOCAL -as "nexus" -o ot_350

File "/root/physcraper_27072020/venv3/bin/physcraper_run.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/root/physcraper_27072020/physcraper-main/bin/physcraper_run.py", line 220, in
scraper.calculate_final_tree(boot_reps = boot_reps)
File "/root/physcraper_27072020/physcraper-main/physcraper/scrape.py", line 1218, in calculate_final_tree
self.replace_tre(sumtreepath, schema="nexus")
File "/root/physcraper_27072020/physcraper-main/physcraper/scrape.py", line 959, in replace_tre
rooted_tre = root_tree_from_synth(newtre, self.data.otu_dict)
File "/root/physcraper_27072020/physcraper-main/physcraper/opentree_helpers.py", line 54, in root_tree_from_synth
tax_mrca = OT.taxon_mrca(spp).response_dict['mrca']['ott_id']
File "/root/physcraper_27072020/venv3/src/opentree/opentree/ot_object.py", line 263, in taxon_mrca
call_record = self.ws.taxonomy_mrca(ott_ids=ott_ids)
File "/root/physcraper_27072020/venv3/src/opentree/opentree/ot_ws_wrapper.py", line 79, in taxonomy_mrca
d = {"ott_ids": [int(i) for i in ott_ids]}
File "/root/physcraper_27072020/venv3/src/opentree/opentree/ot_ws_wrapper.py", line 79, in
d = {"ott_ids": [int(i) for i in ott_ids]}
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

[snacktavish]

I'm having trouble re-creating this bug. It seems like it may be due to the version of the python-opentree dependency. Could you paste the output of pip freeze?

[mkandziora]

I realized I run this one on an older commit - rerunning it on one from last weekend.

Nevertheless, this is my pip freeze output (for the virtualenv I created and setup physcraper a couple of weeks ago):

alabaster==0.7.12
apipkg==1.5
attrs==19.3.0
Babel==2.8.0
biopython==1.76
certifi==2020.6.20
chardet==3.0.4
commonmark==0.9.1
configparser==5.0.0
coverage==5.1
DateTime==4.3
DendroPy==4.4.0
docutils==0.16
execnet==1.7.1
future==0.18.2
idna==2.9
imagesize==1.2.0
importlib-metadata==1.7.0
Jinja2==2.11.2
m2r==0.2.1
MarkupSafe==1.1.1
mistune==0.8.4
more-itertools==8.4.0
numpy==1.19.0
-e git+https://github.com/OpenTreeOfLife/python-opentree@093489f0b1c18119f404b2c5450dbc35880fe2f6#egg=opentree
packaging==20.4
pandas==1.0.5

Editable install with no version control (Physcraper==0.1)

-e /root/physcraper_27072020/physcraper-main
pkg-resources==0.0.0
pluggy==0.13.1
py==1.9.0
Pygments==2.6.1
pyparsing==2.4.7
pytest==5.4.3
pytest-cov==2.10.0
pytest-forked==1.2.0
pytest-xdist==1.32.0
python-dateutil==2.8.1
pytz==2020.1
recommonmark==0.6.0
requests==2.24.0
sh==1.13.1
six==1.15.0
snowballstemmer==2.0.0
Sphinx==3.1.1
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==1.0.3
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.4
urllib3==1.25.9
wcwidth==0.2.5
zipp==3.1.0
zope.interface==5.1.0

[snacktavish]

Thanks! Let me know how it goes on the newer commit. The python-opentree version looks fine, which is what I had guessed might be the issue.