pokey / geneinfo

Get papers and info about genes

Hi there 👋

I build open-source voice coding tools like Cursorless. Lately, I've been obsessed with the following question:

How can we leverage the phenomenal power of human language to interact with code in new ways?

I'm working on a spoken language for large-scale, structurally aware voice-controlled code generation and refactoring.

If that excites you, get involved! Comment on the issues, comment on my videos, hack on some code, join the Talon slack, tweet at me, and consider sponsoring me 😊

geneinfo's Issues

[Errno 65] Cannot connect to host

• Gene Info version: unknown (1.0 ?)
• Python version: python3
• Operating System: macOS Sierra

Description

##Describe what you were trying to get done.

I was attempting to run the script in terminal after successfully completing all steps in the README.md file.

##Tell us what happened, what went wrong, and what you expected to happen.

The script runs for 0-70% (typically), before throwing an error, ending in "Cannot connect to host eutils.ncbi.nlm.nih.gov:443 ssl:True [Can not connect to eutils.ncbi.nlm.nih.gov:443 [No route to host]]"

The amount of progress made by the script is variable, and I have had the script complete once before (1 out of approx 50 attempts).

What I Did

##Paste the command(s) you ran and the output.
##If there was a crash, please include the traceback here.

geneinfo --genes genes.txt --terms terms.txt --extra-term regulation
  3%|█████▌                                                                                                                                                               | 1/30 [00:00<00:13,  2.23query/s]
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/aiohttp/connector.py", line 710, in _create_direct_connection
    local_addr=self._local_addr)
  File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/base_events.py", line 776, in create_connection
    raise exceptions[0]
  File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/base_events.py", line 763, in create_connection
    yield from self.sock_connect(sock, address)
  File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/selector_events.py", line 451, in sock_connect
    return (yield from fut)
  File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/selector_events.py", line 456, in _sock_connect
    sock.connect(address)
OSError: [Errno 65] No route to host

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/aiohttp/connector.py", line 378, in connect
    proto = yield from self._create_connection(req)
  File "/usr/local/lib/python3.6/site-packages/aiohttp/connector.py", line 687, in _create_connection
    _, proto = yield from self._create_direct_connection(req)
  File "/usr/local/lib/python3.6/site-packages/aiohttp/connector.py", line 737, in _create_direct_connection
    (req.host, req.port, exc.strerror)) from exc
aiohttp.client_exceptions.ClientConnectorError: [Errno 65] Can not connect to eutils.ncbi.nlm.nih.gov:443 [No route to host]

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/bin/geneinfo", line 11, in <module>
    load_entry_point('geneinfo', 'console_scripts', 'geneinfo')()
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/webbert/Dropbox (Personal)/Work Life/Crick PhD/My work/Subclonal Drivers/Late_Subclonal Driver genes/201612 Literature review of 87 genes/20161219 Pubmed search tool/geneinfo-master/geneinfo/cli.py", line 31, in main
    extra_term))
  File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/base_events.py", line 466, in run_until_complete
    return future.result()
  File "/Users/webbert/Dropbox (Personal)/Work Life/Crick PhD/My work/Subclonal Drivers/Late_Subclonal Driver genes/201612 Literature review of 87 genes/20161219 Pubmed search tool/geneinfo-master/geneinfo/geneinfo.py", line 84, in process_genes
    for gene in group
  File "/Users/webbert/Dropbox (Personal)/Work Life/Crick PhD/My work/Subclonal Drivers/Late_Subclonal Driver genes/201612 Literature review of 87 genes/20161219 Pubmed search tool/geneinfo-master/geneinfo/geneinfo.py", line 23, in process_gene
    for term in terms
  File "/Users/webbert/Dropbox (Personal)/Work Life/Crick PhD/My work/Subclonal Drivers/Late_Subclonal Driver genes/201612 Literature review of 87 genes/20161219 Pubmed search tool/geneinfo-master/geneinfo/geneinfo.py", line 51, in process_search
    for data in await asyncio.gather(*fetcher.get_pages()):
  File "/usr/local/lib/python3.6/site-packages/pubmedasync/fetch.py", line 61, in _get
    async with self.session.get(url) as resp:
  File "/usr/local/lib/python3.6/site-packages/aiohttp/client.py", line 636, in __aenter__
    self._resp = yield from self._coro
  File "/usr/local/lib/python3.6/site-packages/aiohttp/client.py", line 230, in _request
    conn = yield from self._connector.connect(req)
  File "/usr/local/lib/python3.6/site-packages/aiohttp/connector.py", line 383, in connect
    .format(key, exc.strerror)) from exc
aiohttp.client_exceptions.ClientConnectorError: [Errno 65] Cannot connect to host eutils.ncbi.nlm.nih.gov:443 ssl:True [Can not connect to eutils.ncbi.nlm.nih.gov:443 [No route to host]]