gemini plugin

[ramaniak]

Hello, I recently installed puzzle and was hoping to view a gemini db with it.

The install was fine ( I think). There are a couple of warning with the flask import and I am not sure if these are important?

puzzle --help

/Library/Python/2.7/site-packages/flask/exthook.py:71: ExtDeprecationWarning: Importing flask.ext.markdown is deprecated, use flask_markdown instead.
  .format(x=modname), ExtDeprecationWarning
/Library/Python/2.7/site-packages/flask/exthook.py:106: ExtDeprecationWarning: Detected extension named flaskext.markdown, please rename it to flask_markdown. The old form is deprecated.
  .format(x=modname), ExtDeprecationWarning
Usage: puzzle [OPTIONS] COMMAND [ARGS]...

  Puzzle: manage DNA variant resources.

Options:
  --version          Show the version and exit.
  -v, --verbose
  -c, --config PATH
  --help             Show this message and exit.

Commands:
  cases        Show all cases in the database.
  delete       Delete a case or individual from the...
  individuals  Show all individuals in the database.
  init         Initialize a database that store metadata...
  load         Load a variant source into the database.
  view         Visualize DNA variant resources.

I then ran the test as below and got the error: "TypeError: Expected bytes, got path"

puzzle view tests/fixtures/

and this seemed to go away if I gave it a path to a vcf instead of a folder. Though, I am not sure why this was not working.

Finally, the real reason I am posting this. I have a gemini db that I would like to view and ran it as below

puzzle view batch1-gatk-haplotype.db 

this gives the following error:

/Library/Python/2.7/site-packages/flask/exthook.py:71: ExtDeprecationWarning: Importing flask.ext.markdown is deprecated, use flask_markdown instead.
  .format(x=modname), ExtDeprecationWarning
/Library/Python/2.7/site-packages/flask/exthook.py:106: ExtDeprecationWarning: Detected extension named flaskext.markdown, please rename it to flask_markdown. The old form is deprecated.
  .format(x=modname), ExtDeprecationWarning
[2016-06-22 16:49:32,868] puzzle.cli.view           INFO     Using in memory database
[2016-06-22 16:49:32,870] puzzle.cli.view           INFO     building database: /var/folders/_9/kw4cn4xn4x34tjpkm0985c1c0000gp/T/tmpvgs_TJ/puzzle.sqlite3
[2016-06-22 16:49:32,880] puzzle.plugins.sql.store  INFO     Creating database
[2016-06-22 16:49:32,898] puzzle.cli.view           ERROR    Need to have gemini installed to use gemini plugin
Aborted!

It's complaining about gemini not being there, but I do have gemini in my path

which gemini
/usr/local/bin//gemini

and this also in my bashrc. I am trying to figure out how to get puzzle to load the gemini database. Any help is much appreciated.

Thanks Arun

[moonso]

Hi Arun,

you need to have the python package gemini installed, we use this to access gemini databases through it's python api. If you can do:

$ python
Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec  6 2015, 18:57:58)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gemini
>>>

it should work.

For the other problems we will have a look to see what is going on.

Regards,

Måns

[ramaniak]

Hello Måns

Thanks. On further digging and running py.test test/ I get the attached log. What stands out are the following errors:

---

tests/plugins/gemini/test_gemini_case_mixin.py:1: in from puzzle.plugins import GeminiPlugin

E ImportError: cannot import name GeminiPlugin

---

E KeyError: 'PHENOMIZER_AUTH'

---

"NameError: global name 'GeminiQuery' is not defined"

Does this give you any indication on what's going on?

Thanks for your attention to this issue.

Arun

On Wed, Jun 29, 2016 at 2:37 AM, Måns Magnusson notifications@github.com wrote:

Hi Arun,

you need to have the python package gemini installed, we use this to access gemini databases through it's python api. If you can do:

$ python Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6 2015, 18:57:58) [GCC 4.2.1 (Apple Inc. build 5577)] on darwin Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please check out: http://continuum.io/thanks and https://anaconda.org

import gemini

it should work.

For the other problems we will have a look to see what is going on.

Regards,

Måns

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