exception running basic pyensembl install command

[ghost]

Hello

I'm just getting started using pyensembl and I'm unable to run the initial install command: pyensembl install --release 87 --species human

Any advice etc. on getting this working much appreciated, more details below.

I get the following output / stacktrace:

2018-06-27 11:44:32,747 - pyensembl.shell - INFO - Running 'install' for EnsemblRelease(release=87, species='homo_sapiens')
2018-06-27 11:44:32,748 - pyensembl.download_cache - INFO - Fetching /Users/davelahr/pyensembl/pyensembl/GRCh38/ensembl87/Homo_sapiens.GRCh38.87.gtf.gz from URL ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz
Traceback (most recent call last):
  File "/Users/davelahr/miniconda2/envs/pyensembl/bin/pyensembl", line 11, in <module>
    sys.exit(run())
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/shell.py", line 169, in run
    genome.download(overwrite=args.overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/genome.py", line 235, in download
    self._set_local_paths(download_if_missing=True, overwrite=overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/genome.py", line 216, in _set_local_paths
    overwrite=overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/genome.py", line 180, in _get_gtf_path
    overwrite=overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/genome.py", line 173, in _get_cached_path
    overwrite=overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/download_cache.py", line 295, in local_path_or_install_error
    overwrite=overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/download_cache.py", line 270, in download_or_copy_if_necessary
    overwrite)
  File "/Users/davelahr/miniconda2/envs/pyensembl/lib/python3.6/site-packages/pyensembl/download_cache.py", line 218, in _download_if_necessary
    download_url=url)
TypeError: _download() got an unexpected keyword argument 'filename'

My setup:

1. created an environment using miniconda with pip
   • python version 3.6.5
2. pip install pyensembl - version 1.2.6
   • final line of output: Successfully installed appdirs-1.4.3 chardet-3.0.4 datacache-1.0.0 gtfparse-1.0.7 idna-2.7 memoized-property-1.0.3 mock-2.0.0 numpy-1.14.5 pandas-0.23.1 pbr-4.0.4 progressbar33-2.4 pyensembl-1.2.6 python-dateutil-2.7.3 pytz-2018.4 requests-2.19.1 serializable-0.1.1 simplejson-3.15.0 six-1.11.0 tinytimer-0.0.0 typechecks-0.1.0 urllib3-1.23

[ai4pharma]

I have the same problem. It seems caused by line 218 of pyensembl/download_cache.py, which is

            datacache.download._download(
                filename=local_filename,
                full_path=cached_path,
                download_url=url)

However, when I check datacache/download.py, the _download function is

def _download(download_url, timeout=None):
    if download_url.startswith("http"):
        response = requests.get(download_url, timeout=timeout)
        response.raise_for_status()
        return response.content

It only require download_url, does't require filename and full_path argument

[bbreton]

I believe manually downgrading datacache to 0.5.5 from 1.0.0 will fix this issue until the devs get a chance to fix it. Hopefully doing this doesn't cause problems elsewhere as I didn't run full testing on it.

pip install --upgrade datacache==0.5.5

[ghost]

Thank you, that worked for me!

[iskandr]

Sorry for the breakage @bbreton and @dllahr-foghorntx! A PR got stuck because of https://github.com/openvax/pyensembl/issues/201. I just merged the necessary PR to fix the install command and will work on figuring out Travis later.

[samleenz]

Hi @iskandr, I still have this issue using the bioconda install of pyensembl v=1.2.6 for python 3.6. When I look at the download_cache.py file I see the fix from #191 is not present (lines 214-218). Do you know when the conda version will be updated to fix this?

[iskandr]

Hey @samleenz -- we currently only auto-submit new PyEnsembl version to PyPI so the conda versions are likely being maintained by someone else (e.g. https://anaconda.org/edurand/pyensembl). I can look into adding support for conda.

[samleenz]

Ah, didn't notice that - apologies! If you do end up adding pyensembl to conda that would be very appreciated but if not i can make the pip version work.