LaTeX equations should use (α^0)_(p,P_GFP), not α_(p,P_GFP)

[hgscott]

In the Supplementary S1, the production rate symbol α_(p,P_GFP)of formula (17), (25), (31), (41), (47), (59), (65), (79), (85), (101), and (107) should be changed to the maximal production rate symbol (α^0)_(p,P_GFP).

[hgscott]

I am unsure how to do this directly in the latex_generation script, since I don't want to change all of the alpha_ps (e.g. the alpha_p,P_dCas9 should still be alpha_p, not alpha^0_p.

So, I want to add an addendum to the sbol_to_latex.py script that will change the output of the latex_generation function before saving it to the generated_equations.tex file.

But, I can no longer run my existing sbol_to_latex.py script, I am getting an error due to the tyto package.

The simplest recreation of the error, is when I run:

import tyto

tyto.SBO.systems_biology_representation

I get the following error message:

Traceback (most recent call last):
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 1346, in do_open
    h.request(req.get_method(), req.selector, req.data, headers,
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/http/client.py", line 1285, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/http/client.py", line 1331, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/http/client.py", line 1280, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/http/client.py", line 1040, in _send_output
    self.send(msg)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/http/client.py", line 980, in send
    self.connect()
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/http/client.py", line 946, in connect
    self.sock = self._create_connection(
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/socket.py", line 844, in create_connection
    raise err
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/socket.py", line 832, in create_connection
    sock.connect(sa)
ConnectionRefusedError: [Errno 61] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/tyto/tyto.py", line 47, in __getattr__
    return self.__getattribute__('get_uri_by_term')(name)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/tyto/tyto.py", line 123, in get_uri_by_term
    uri = self._handler('get_uri_by_term', exception, sanitized_term)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/tyto/tyto.py", line 72, in _handler
    response = method(self, *args)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/tyto/endpoint/endpoint.py", line 81, in get_uri_by_term
    response = self.query(ontology, query, error_msg)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/tyto/endpoint/endpoint.py", line 298, in query
    response = super().query(ontology, sparql, err_msg)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/tyto/endpoint/endpoint.py", line 231, in query
    response = self._endpoint.query()
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/SPARQLWrapper/Wrapper.py", line 960, in query
    return QueryResult(self._query())
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/site-packages/SPARQLWrapper/Wrapper.py", line 926, in _query
    response = urlopener(request)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 214, in urlopen
    return opener.open(url, data, timeout)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 517, in open
    response = self._open(req, data)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 534, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 494, in _call_chain
    result = func(*args)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 1375, in http_open
    return self.do_open(http.client.HTTPConnection, req)
  File "/Users/hscott/Documents/APT/CRISPRi-promoters/env/lib/python3.9/urllib/request.py", line 1349, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 61] Connection refused>

So for now, I have corrected the equations manually in a new file called manually_edited_equations.tex, but I would like to revisit this so that the equations are fixed in the automatic generation.

[hgscott]

To debug why tyto isn't working for me, I made a completely new conda environment, tyto-test, with: conda create -n tyto-test python=3

Then I installed tyto wth pip.

Then I ran my minimal test from above:

And I got the same error, ending with:

[hgscott]

On safari, when I try to navigate to Ontobee.org, I get an error that the server is down:

[hgscott]

Ontobee is now back up, and so we can now do the pretty fix.