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nrasulicpfmRajmund Csombordi
nrasulicpfm
and
Rajmund Csombordi
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[EDPEV-2767] Fix login issues (#484)
* move code from quartzbio client * Patched login debug fix --------- Co-authored-by: Rajmund Csombordi <rajmund.csombordi@precisionformedicine.com>
1 parent 70605d0 commit d3936c0

15 files changed

Lines changed: 372 additions & 222 deletions

‎solvebio/__init__.py‎

Lines changed: 61 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -22,17 +22,6 @@
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# Python 2.6 doesn't support this
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pass
2424

25-
# Read/Write API key
26-
api_key = _os.environ.get('SOLVEBIO_API_KEY', None)
27-
# OAuth2 access tokens
28-
access_token = _os.environ.get('SOLVEBIO_ACCESS_TOKEN', None)
29-
if access_token is None:
30-
access_token = _os.environ.get('EDP_ACCESS_TOKEN', None)
31-
32-
api_host = _os.environ.get('SOLVEBIO_API_HOST', None)
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if api_host is None:
34-
api_host = _os.environ.get('EDP_API_HOST', 'https://api.solvebio.com')
35-
3625

3726
def help():
3827
_open_help('/docs')
@@ -99,7 +88,8 @@ def emit(self, record):
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from .query import Query, BatchQuery, Filter, GenomicFilter
10089
from .global_search import GlobalSearch
10190
from .annotate import Annotator, Expression
102-
from .client import SolveClient
91+
from .client import client, SolveClient
92+
from .auth import authenticate
10393
from .resource import (
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Application,
10595
Beacon,
@@ -125,53 +115,69 @@ def emit(self, record):
125115
)
126116

127117

128-
def login(**kwargs):
118+
def login(
119+
api_host: str = None,
120+
api_key: str = None,
121+
access_token: str = None,
122+
name: str = None,
123+
version: str = None,
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debug: bool = False,
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):
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"""
127+
Function to login to the QuartzBio/EDP API when using EDP in a python script.
128+
Note that another function is used when CLI command `quartzbio login` is used!
129+
EDP checks user credentials & host URL from multiple sources, in the following order:
130+
131+
1) Parameters provided (e.g. the parameters of this function)
132+
2) Environment variables (if the above parameters weren't provided)
133+
3) quartzbio credentials file stored in the user's HOME directory
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(if parameters and environment variables weren't found)
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136+
:param api_host: the QuartzBio EDP instance's URL to access.
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:param access_token: your user's access token, which you can generate at the EDP website
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(user menu > `Personal Access Tokens`)
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:param api_key: Your API key. You can use this instead of providing an access token
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:param name: name
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:param version: version
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Example:
144+
.. code-block:: python
145+
146+
import quartzbio
147+
quartzbio.login(
148+
api_host="https://solvebio.api.az.aws.quartz.bio",
149+
api_key=YOUR_API_KEY
150+
)
129151
"""
130-
Sets up the auth credentials using the provided key/token,
131-
or checks the credentials file (if no token provided).
152+
token_type = None
153+
token = None
132154

133-
Lookup order:
134-
1. access_token
135-
2. api_key
136-
3. local credentials
155+
if access_token:
156+
token_type = "Bearer"
157+
token = access_token
158+
elif api_key:
159+
token_type = "Token"
160+
token = api_key
137161

138-
No errors are raised if no key is found.
139-
"""
140-
from .cli.auth import get_credentials
141-
global access_token, api_key, api_host
142-
143-
# Clear any existing auth keys
144-
access_token, api_key = None, None
145-
# Update the host
146-
api_host = kwargs.get('api_host') or api_host
147-
148-
if kwargs.get('access_token'):
149-
access_token = kwargs.get('access_token')
150-
elif kwargs.get('api_key'):
151-
api_key = kwargs.get('api_key')
152-
else:
153-
creds = get_credentials()
154-
# creds = (host, email, token_type, token)
155-
if creds:
156-
api_host = creds[0]
157-
if creds[2] == 'Bearer':
158-
access_token = creds[3]
159-
else:
160-
# By default, assume it is an API key.
161-
api_key = creds[3]
162-
163-
# Always update the client host, version and agent
164-
from solvebio.client import client
165-
client.set_host()
166-
client.set_user_agent(name=kwargs.get('name'),
167-
version=kwargs.get('version'))
168-
169-
if not (api_key or access_token):
170-
return False
162+
if api_host or token or debug:
163+
client._host, client._auth = authenticate(
164+
api_host, token, token_type=token_type, debug=debug
165+
)
166+
167+
client.set_user_agent(name=name, version=version)
168+
169+
170+
def whoami():
171+
try:
172+
user = client.whoami()
173+
except Exception as e:
174+
print("{} (code: {})".format(e.message, e.status_code))
171175
else:
172-
# Update the client token
173-
client.set_token()
174-
return True
176+
return user
177+
178+
179+
def get_api_host():
180+
return client._host
175181

176182

177183
__all__ = [

‎solvebio/__main__.py‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
2+
import sys
3+
4+
from .cli.main import main
5+
6+
if __name__ == "__main__":
7+
main(sys.argv[1:])

‎solvebio/auth.py‎

Lines changed: 183 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,183 @@
1+
from __future__ import absolute_import
2+
3+
import os
4+
from typing import Literal, Tuple
5+
6+
from six.moves.urllib.parse import urlparse
7+
8+
import logging
9+
10+
from requests.auth import AuthBase
11+
import requests
12+
13+
from solvebio import SolveError
14+
from solvebio.cli.credentials import get_credentials
15+
16+
logger = logging.getLogger("solvebio")
17+
18+
19+
class SolveBioTokenAuth(AuthBase):
20+
"""Custom auth handler for SolveBio API token authentication"""
21+
22+
def __init__(self, token=None, token_type="Token"):
23+
self.token = token
24+
self.token_type = token_type
25+
26+
def __call__(self, r):
27+
if self.token:
28+
r.headers["Authorization"] = "{0} {1}".format(self.token_type, self.token)
29+
return r
30+
31+
def __repr__(self):
32+
if self.token:
33+
return self.token_type
34+
else:
35+
return "Anonymous"
36+
37+
38+
def authenticate(
39+
host: str,
40+
token: str,
41+
token_type: Literal["Bearer", "Token"],
42+
*,
43+
raise_on_missing: bool = True,
44+
debug: bool = False
45+
) -> Tuple[str, SolveBioTokenAuth]:
46+
"""
47+
Sets login credentials for SolveBio API authentication.
48+
49+
:param str host: API host url
50+
:param str token: API access token or API key
51+
:param str token_type: API token type. `Bearer` is used for access tokens, while `Token` is used for API Keys.
52+
:param bool raise_on_missing: Raise an exception if no credentials are available.
53+
"""
54+
# used for debugging
55+
source_host = None
56+
source_token = None
57+
58+
# Find credentials from environment variables
59+
if not host:
60+
host = (
61+
os.environ.get("QUARTZBIO_API_HOST", None)
62+
or os.environ.get("EDP_API_HOST", None)
63+
or os.environ.get("SOLVEBIO_API_HOST", None)
64+
)
65+
66+
if not token:
67+
api_key = (
68+
os.environ.get("QUARTZBIO_API_KEY", None)
69+
or os.environ.get("EDP_API_KEY", None)
70+
or os.environ.get("SOLVEBIO_API_KEY", None)
71+
)
72+
73+
access_token = (
74+
os.environ.get("QUARTZ_ACCESS_TOKEN", None)
75+
or os.environ.get("EDP_ACCESS_TOKEN", None)
76+
or os.environ.get("SOLVEBIO_ACCESS_TOKEN", None)
77+
)
78+
79+
if access_token:
80+
token = access_token
81+
token_type = "Bearer"
82+
elif api_key:
83+
token = api_key
84+
token_type = "Token"
85+
86+
if token:
87+
source_token = 'envvars'
88+
else:
89+
source_token = 'params'
90+
91+
# Find credentials from local credentials file
92+
if not token:
93+
if creds := get_credentials(host):
94+
token_type = creds.token_type
95+
token = creds.token
96+
97+
if host is None:
98+
# this happens when user/ennvars provided no API host for the login command
99+
# but the credentials file still contains login credentials
100+
host = creds.api_host
101+
102+
if host:
103+
source_host = 'creds'
104+
if token:
105+
source_token = 'creds'
106+
107+
if (not host and raise_on_missing) or debug:
108+
# this will tell the user where QB Client found the credentials from
109+
creds_path = netrc.path()
110+
print('\n'.join([
111+
"Login Debug:",
112+
f"--> Host: {host}\n (source: {source_host})",
113+
f"--> Token Type: {token_type}\n (source: {source_token})",
114+
"\n1) source: params",
115+
" Means that you've passed this through the login CLI command:",
116+
" quartzbio login --host <EDP_HOST> --access_token <EDP_TOKEN>",
117+
"\n or the quartzbio.login function:",
118+
" import quartzbio",
119+
" quartzbio.login(debug=True)",
120+
"\n2) source: creds",
121+
" Means that the QB client has saved your credentials in:",
122+
f" {creds_path}",
123+
"\n3) source: envvars",
124+
" Means that you've set your credentials through environment variables:",
125+
" QUARTZBIO_API_HOST",
126+
" QUARTZBIO_ACCESS_TOKEN",
127+
" QUARTZBIO_API_KEY",
128+
]))
129+
130+
if not debug:
131+
raise SolveError("No SolveBio API host is set")
132+
133+
host = validate_api_host_url(host)
134+
135+
# If the domain ends with .solvebio.com, determine if
136+
# we are being redirected. If so, update the url with the new host
137+
# and log a warning.
138+
if host and host.rstrip("/").endswith(".api.solvebio.com"):
139+
old_host = host.rstrip("/")
140+
response = requests.head(old_host, allow_redirects=True)
141+
# Strip the port number from the host for comparison
142+
new_host = validate_api_host_url(response.url).rstrip("/").replace(":443", "")
143+
144+
if old_host != new_host:
145+
logger.warning(
146+
'API host redirected from "{}" to "{}", '
147+
"please update your local credentials file".format(old_host, new_host)
148+
)
149+
host = new_host
150+
151+
if token is not None:
152+
auth = SolveBioTokenAuth(token, token_type)
153+
else:
154+
auth = None
155+
156+
# TODO: warn user if WWW url is provided in edp_login!
157+
158+
# @TODO: remove references to solvebio.api_host, etc...
159+
160+
return host, auth
161+
162+
163+
def validate_api_host_url(url):
164+
"""
165+
Validate SolveBio API host url.
166+
167+
Valid urls must not be empty and
168+
must contain either HTTP or HTTPS scheme.
169+
"""
170+
171+
# Default to https if no scheme is set
172+
if "://" not in url:
173+
url = "https://" + url
174+
175+
parsed = urlparse(url)
176+
if parsed.scheme not in ["http", "https"]:
177+
raise SolveError(
178+
"Invalid API host: %s. " "Missing url scheme (HTTP or HTTPS)." % url
179+
)
180+
elif not parsed.netloc:
181+
raise SolveError("Invalid API host: %s." % url)
182+
183+
return parsed.geturl()

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