paulhoule / gastrodon Goto Github PK

On a clean restart:
import gastrodon
produces
Traceback (most recent call last): File "<input>", line 1, in <module> File "C:\Program Files\JetBrains\PyCharm Community Edition with Anaconda plugin 2020.1\plugins\python-ce\helpers\pydev\_pydev_bundle\pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "C:\Users\andyt\anaconda3\envs\Property\lib\site-packages\gastrodon\__init__.py", line 13, in <module> from typing import Dict,GenericMeta,Match ImportError: cannot import name 'GenericMeta' from 'typing' (C:\Users\andyt\anaconda3\envs\Property\lib\typing.py)

running the same in Jupyter gives a little more info:
`ImportError Traceback (most recent call last)
in
----> 1 import gastrodon

~\anaconda3\lib\site-packages\gastrodon_init_.py in
11 from types import FunctionType,LambdaType,GeneratorType,CoroutineType,FrameType,CodeType,MethodType
12 from types import BuiltinFunctionType,BuiltinMethodType,DynamicClassAttribute,ModuleType,AsyncGeneratorType
---> 13 from typing import Dict,GenericMeta,Match
14 from urllib.error import HTTPError
15 from urllib.parse import urlparse

ImportError: cannot import name 'GenericMeta' from 'typing' (C:\Users\andyt\anaconda3\lib\typing.py)`

After playing around a bit with gastrodon, I think I have bumped into some problems regarding column types. To reproduce:

Preliminaries

from gastrodon import RemoteEndpoint, inline
import pandas as pd

prefixes = inline("""
    @prefix : <http://dbpedia.org/resource/> .
    @prefix dbp: <http://dbpedia.org/ontology/> .
    @prefix pr: <http://dbpedia.org/property/> .
    @prefix foaf: <http://xmlns.com/foaf/0.1/> .
""").graph
endpoint = RemoteEndpoint(
    "http://dbpedia.org/sparql/"
    ,default_graph="http://dbpedia.org"
    ,prefixes=prefixes
    ,base_uri="http://dbpedia.org/resource/"
)

Error with dates

endpoint.select("""
SELECT DISTINCT ?personName ?bDay
WHERE {
    ?person a dbp:Person .
    ?person foaf:name ?nombrePersona .
    ?person dbp:birthDate ?bDay .
    }
    LIMIT 10
""")

Output:

Traceback (most recent call last):
  File "<stdin>", line 9, in <module>
  File "/opt/conda/lib/python3.6/site-packages/gastrodon/__init__.py", line 502, in select
    frame=self._dataframe(result)
  File "/opt/conda/lib/python3.6/site-packages/gastrodon/__init__.py", line 397, in _dataframe
    column[key] = self._normalize_column_type(column[key])
  File "/opt/conda/lib/python3.6/site-packages/gastrodon/__init__.py", line 376, in _normalize_column_type
    return [None if x==None else int(x) for x in column]
  File "/opt/conda/lib/python3.6/site-packages/gastrodon/__init__.py", line 376, in <listcomp>
    return [None if x==None else int(x) for x in column]
TypeError: int() argument must be a string, a bytes-like object or a number, not 'datetime.date'

Issue (casting floats)

endpoint.select("""
SELECT DISTINCT ?starName ?mass
WHERE {
    ?star a dbp:Star .
    ?star foaf:name ?starName .
    ?star pr:mass ?mass
} LIMIT 1
""")

Output:

    starName  mass
0  61 Cygni     0

Expected output:

    starName  mass
0  61 Cygni   0.63

(see this)

Possible cause

I believe that they are coming from _normalize_column_type:

1. pd.datetime is not considered, so when trying to do int(x) where x is a pd.datetime, the above error appears.
2. If all elements in the column are float type, they are silently casted into int, as shown in the issue above.

My question now is: is it really necessary to normalize the columns?
pandas is usually smart enough to accommodate column types and cast if needed.
If I skip the _normalize_column_type() in the code, in the previous issue with the stars example, the mass is not casted to int, and if needed to cast to str, it does:

endpoint.select("""
SELECT DISTINCT ?starName ?mass
WHERE {
    ?star a dbp:Star .
    ?star foaf:name ?starName .
    ?star pr:mass ?mass
} LIMIT 100
""").head()

_.mass.dtype

Output:

      starName          mass
0     61 Cygni          0.63
1     61 Cygni           0.7
2  70 Virginis          1.12
3  70 Virginis  >7.49 ± 0.61
4      Albireo           3.2

dtype('O')

Python 3.6.6
gastrodon 0.9.3
pandas 0.23.4

in jupyter notebook, got the below error when doing

import pandas as pd
import io
import numpy as np
from urllib.request import urlopen
import json
from math import *
from platform import python_version
print("Python v "+python_version())
from gastrodon import RemoteEndpoint,QName,ttl,URIRef,inline
from matplotlib import pyplot

<<
Traceback (most recent call last):

File "/usr/local/lib/python3.5/dist-packages/IPython/core/interactiveshell.py", line 3326, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)

File "", line 9, in
from gastrodon import RemoteEndpoint,QName,ttl,URIRef,inline

File "/usr/local/lib/python3.5/dist-packages/gastrodon/init.py", line 136
kwargs:Dict={}
^
SyntaxError: invalid syntax

Any hints ?

Just wanted so thank you for providing this software. It really made someone happy today!

I see in the API documentation that the remote endpoint function can take basic credentials as user name and password. If the endpoint is controlled by individual or group access rights, then you wouldn't want to save the credentials in a shared notebook, however. How can the credentials be passed into Gastrodon from an external source?

Running python -m unittest or coverage run -m unittest discover both raise an ImportError exception:

ImportError: Failed to import test module: gastrodon.domain
Traceback (most recent call last):
  File "/usr/local/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
    package = self._get_module_from_name(name)
  File "/usr/local/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/home/jugurtha/workspace/python/gastrodon/gastrodon/domain/__init__.py", line 11, in <module>
    from sphinx.locale import l_, _
ImportError: cannot import name 'l_' from 'sphinx.locale' (/home/jugurtha/workspace/python/gastrodon/venv/lib/python3.7/site-packages/sphinx/locale/__init__.py)

According to this commit sphinx-doc/sphinx@8d653a4, the l_() function was integrated into _().

Recommended action:

Change the line:

    from sphinx.locale import l_, _

to

    from sphinx.locale import _

Running python -m unittest executes with the following results

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK

Note: The exception mentioned in #9 also was raised, and the proposed changes in mkdocstrings/mkdocstrings#2 were added not to have that error. These are also the changes proposed in #5

I'm stuck using python 3.7. Because GenericMeta is no longer included in typing the import of gastrodon fails. I found a workaround here mkdocstrings/mkdocstrings#2 but I'm not sure if it will work in gastrodon

1- Very very cool project ! Thank you !
I am newbie in Notebooks, how hard/easy is it to integrate

SuRF[link] with Gastrodon? this way no need to write SPARQL manually?

Thank you