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put telemetry on onecodex
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Cindy committed Aug 30, 2017
1 parent 10b980b commit cc73bd0
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Showing 3 changed files with 51 additions and 48 deletions.
41 changes: 12 additions & 29 deletions onecodex/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
author: @mbiokyle29
"""
from __future__ import print_function
from functools import wraps
import logging
import os
import platform
Expand All @@ -17,7 +16,7 @@

from onecodex.utils import (cli_resource_fetcher, download_file_helper,
valid_api_key, OPTION_HELP, pprint,
warn_if_insecure_platform)
warn_if_insecure_platform, telemetry)
from onecodex.api import Api
from onecodex.exceptions import ValidationWarning, ValidationError, UploadException
from onecodex.auth import _login, _logout, _silent_login
Expand Down Expand Up @@ -50,9 +49,19 @@
help=OPTION_HELP['no_telemetry'])
@click.version_option(version=__version__)
@click.pass_context
@telemetry
def onecodex(ctx, api_key, no_pprint, verbose, no_telemetry):
"""One Codex v1 API command line interface"""
print('onecodex')
# set up Sentry
if not (no_telemetry or os.environ.get('ONE_CODEX_NO_TELEMETRY') is not None):
key = 'f74d421bbdb44ea78de504f25067b9a4:16c934ef082e40efaf51958d8521c32d'
try:
client = Client(dsn="https://{}@sentry.onecodex.com/9".format(key), release=__version__)
client.extra_context({'platform': platform.platform()})
ctx.obj['sentry'] = client
except Exception:
pass

# set up the context for sub commands
click.Context.get_usage = click.Context.get_help
ctx.obj = {}
Expand Down Expand Up @@ -81,32 +90,11 @@ def onecodex(ctx, api_key, no_pprint, verbose, no_telemetry):
if ctx.invoked_subcommand != "upload":
warn_if_insecure_platform()

if not (no_telemetry or os.environ.get('ONE_CODEX_NO_TELEMETRY') is not None):
key = 'f74d421bbdb44ea78de504f25067b9a4:16c934ef082e40efaf51958d8521c32d'
client = Client(dsn="https://{}@sentry.onecodex.com/9".format(key), release=__version__)
client.extra_context({'platform': platform.platform()})
ctx.obj['sentry'] = client


def telemetry(fn):
@wraps(fn)
def telemetry_wrapper(*args, **kwargs):
try:
return fn(*args, **kwargs)
except SystemExit as e:
sys.exit(e.code) # make sure we still exit with the proper code
except:
ctx = args[0]
if 'sentry' in ctx.obj:
ctx.obj['sentry'].captureException()
return telemetry_wrapper


# resources
@onecodex.command('analyses')
@click.argument('analyses', nargs=-1, required=False)
@click.pass_context
@telemetry
def analyses(ctx, analyses):
"""Retrieve performed analyses"""
cli_resource_fetcher(ctx, "analyses", analyses)
Expand All @@ -121,7 +109,6 @@ def analyses(ctx, analyses):
help=OPTION_HELP['results'])
@click.pass_context
@click.argument('classifications', nargs=-1, required=False)
@telemetry
def classifications(ctx, classifications, results, readlevel, readlevel_path):
"""Retrieve performed metagenomic classifications"""

Expand Down Expand Up @@ -157,7 +144,6 @@ def classifications(ctx, classifications, results, readlevel, readlevel_path):
@onecodex.command('panels')
@click.pass_context
@click.argument('panels', nargs=-1, required=False)
@telemetry
def panels(ctx, panels):
"""Retrieve performed in silico panel results"""
cli_resource_fetcher(ctx, "panels", panels)
Expand All @@ -166,7 +152,6 @@ def panels(ctx, panels):
@onecodex.command('samples')
@click.pass_context
@click.argument('samples', nargs=-1, required=False)
@telemetry
def samples(ctx, samples):
"""Retrieve uploaded samples"""
cli_resource_fetcher(ctx, "samples", samples)
Expand Down Expand Up @@ -252,7 +237,6 @@ def upload(ctx, files, max_threads, clean, no_interleave, prompt, validate):

@onecodex.command('login')
@click.pass_context
@telemetry
def login(ctx):
"""Add an API key (saved in ~/.onecodex)"""
base_url = os.environ.get("ONE_CODEX_API_BASE", "https://app.onecodex.com")
Expand All @@ -261,7 +245,6 @@ def login(ctx):

@onecodex.command('logout')
@click.pass_context
@telemetry
def logout(ctx):
"""Delete your API key (saved in ~/.onecodex)"""
_logout()
19 changes: 19 additions & 0 deletions onecodex/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
utils.py
author: @mbiokyle29
"""
from functools import wraps
import importlib
import json
import logging
Expand Down Expand Up @@ -194,6 +195,24 @@ def collapse_user(fp):
return abs_path.replace(home_dir, "~")


def telemetry(fn):
@wraps(fn)
def telemetry_wrapper(*args, **kwargs):
try:
return fn(*args, **kwargs)
except SystemExit as e:
ctx = args[0]
if 'sentry' in ctx.obj:
ctx.obj['sentry'].captureException()
sys.exit(e.code) # make sure we still exit with the proper code
except Exception as e:
ctx = args[0]
if 'sentry' in ctx.obj:
ctx.obj['sentry'].captureException()
raise e
return telemetry_wrapper


class ModuleAlias(object):
# Used as a proxy object to attach
# all of a module's __all__ namespace to
Expand Down
39 changes: 20 additions & 19 deletions tests/test_cli.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,15 +40,15 @@ def test_cli_wo_override(api_data, monkeypatch):

# Analyses
def test_analysis_help(runner, api_data, mocked_creds_file):
result = runner.invoke(Cli, ['analyses', '--help'])
result = runner.invoke(Cli, ['--no-telemetry', 'analyses', '--help'])
analysis_desc = "Retrieve performed analyses"
assert result.exit_code == 0
assert analysis_desc in result.output


def test_analyses(runner, api_data, mocked_creds_file):
r0 = runner.invoke(Cli, ['analyses'])
r1 = runner.invoke(Cli, ['analyses', '593601a797914cbf'])
r0 = runner.invoke(Cli, ['--no-telemetry', 'analyses'])
r1 = runner.invoke(Cli, ['--no-telemetry', 'analyses', '593601a797914cbf'])
assert r0.exit_code == 0
assert r1.exit_code == 0
assert API_DATA['GET::api/v1/analyses/593601a797914cbf']['$uri'] in r0.output
Expand All @@ -57,27 +57,27 @@ def test_analyses(runner, api_data, mocked_creds_file):

# Classifications
def test_classification_instance(runner, api_data, mocked_creds_file):
result = runner.invoke(Cli, ['classifications', '593601a797914cbf'])
result = runner.invoke(Cli, ['--no-telemetry', 'classifications', '593601a797914cbf'])
assert result.exit_code == 0
assert API_DATA['GET::api/v1/classifications/593601a797914cbf']['$uri'] in result.output


def test_classifications_table(runner, api_data, mocked_creds_file, monkeypatch):
result = runner.invoke(Cli, ['classifications', '45a573fb7833449a', '--results'])
result = runner.invoke(Cli, ['--no-telemetry', 'classifications', '45a573fb7833449a', '--results'])
assert result.exit_code == 0
assert "Staphylococcus" in result.output


# Panels
def test_panel_instances(runner, api_data, mocked_creds_file):
result = runner.invoke(Cli, ['panels'])
result = runner.invoke(Cli, ['--no-telemetry', 'panels'])
assert result.exit_code == 0


# Samples
def test_samples(runner, api_data, mocked_creds_file):
r0 = runner.invoke(Cli, ['samples'])
r1 = runner.invoke(Cli, ['samples', '7428cca4a3a04a8e'])
r0 = runner.invoke(Cli, ['--no-telemetry', 'samples'])
r1 = runner.invoke(Cli, ['--no-telemetry', 'samples', '7428cca4a3a04a8e'])
assert r0.exit_code == 0
assert r1.exit_code == 0
assert API_DATA['GET::api/v1/samples/7428cca4a3a04a8e']['$uri'] in r0.output
Expand All @@ -102,7 +102,7 @@ def test_api_login(runner, mocked_creds_path):
login_input = 'user@example.com' + '\n' + 'userpassword' + '\n'
successful_login_msg = 'Your ~/.onecodex credentials file was successfully created.'
with Replace('onecodex.auth.fetch_api_key_from_uname', mock_fetch_api_key):
result = runner.invoke(Cli, ['login'], input=login_input)
result = runner.invoke(Cli, ['--no-telemetry', 'login'], input=login_input)
assert result.exit_code == 0
assert successful_login_msg in result.output

Expand All @@ -112,15 +112,15 @@ def test_creds_file_exists(runner, mocked_creds_file):
make_creds_file()
expected_message = "Credentials file already exists"

result = runner.invoke(Cli, ["login"])
result = runner.invoke(Cli, ['--no-telemetry', "login"])
assert result.exit_code == 0
assert expected_message in result.output


def test_silent_login(runner, mocked_creds_file, api_data):
with runner.isolated_filesystem():
make_creds_file()
result = runner.invoke(Cli, ['samples'])
result = runner.invoke(Cli, ['--no-telemetry', 'samples'])
assert result.exit_code == 0


Expand All @@ -140,15 +140,15 @@ def test_logout_creds_exists(runner, mocked_creds_file):
make_creds_file()
expected_message = "Successfully removed One Codex credentials."
path = os.path.expanduser("~/.onecodex")
result = runner.invoke(Cli, ["logout"])
result = runner.invoke(Cli, ['--no-telemetry', 'logout'])
assert result.exit_code == 0
assert expected_message in result.output
assert os.path.exists(path) is False


def test_logout_creds_dne(runner, mocked_creds_path):
expected_message = "No One Codex API keys found."
result = runner.invoke(Cli, ["logout"])
result = runner.invoke(Cli, ['--no-telemetry', 'logout'])
assert result.exit_code == 1
assert expected_message in result.output

Expand All @@ -169,7 +169,7 @@ def test_standard_uploads(runner, upload_mocks, files, threads):
(but not files >5GB)
"""
with runner.isolated_filesystem():
args = ['--api-key', '01234567890123456789012345678901', 'upload']
args = ['--no-telemetry', '--api-key', '01234567890123456789012345678901', 'upload']
if not threads:
args += ['--max-threads', '1']
for f in files:
Expand All @@ -188,7 +188,7 @@ def test_empty_upload(runner, upload_mocks):
f = 'tmp.fa'
f_out = open(f, mode='w')
f_out.close()
args = ['--api-key', '01234567890123456789012345678901', 'upload', f]
args = ['--no-telemetry', '--api-key', '01234567890123456789012345678901', 'upload', f]
result = runner.invoke(Cli, args)
assert result.exit_code != 0

Expand All @@ -204,7 +204,7 @@ def test_paired_files(runner, upload_mocks):
f_out2.write('>Test fasta\n')
f_out2.write(SEQUENCE)

args = ['--api-key', '01234567890123456789012345678901', 'upload', f, f2]
args = ['--no-telemetry', '--api-key', '01234567890123456789012345678901', 'upload', f, f2]
# check that only one upload is kicked off for the pair of files
patch1 = 'onecodex.lib.upload.upload_file'
patch2 = 'onecodex.lib.inline_validator.FASTXTranslator.close'
Expand All @@ -216,13 +216,13 @@ def test_paired_files(runner, upload_mocks):
assert result.exit_code == 0

# Check with validate=False, should fail
args = ['--api-key', '01234567890123456789012345678901', 'upload', f, f2,
args = ['--no-telemetry', '--api-key', '01234567890123456789012345678901', 'upload', f, f2,
'--do-not-validate']
result2 = runner.invoke(Cli, args)
assert result2.exit_code != 0

# Check with validate=False, interleave=False, should success
args = ['--api-key', '01234567890123456789012345678901', 'upload', f, f2,
args = ['--no-telemetry', '--api-key', '01234567890123456789012345678901', 'upload', f, f2,
'--do-not-validate', '--do-not-interleave']
with mock.patch(patch1) as mp:
result3 = runner.invoke(Cli, args)
Expand All @@ -248,7 +248,8 @@ def mockfilesize(path):
f.write('>BIG!!!\n')
f.write(SEQUENCE)

args = ['--api-key', '01234567890123456789012345678901', 'upload', big_file]
args = ['--no-telemetry', '--api-key',
'01234567890123456789012345678901', 'upload', big_file]

def side_effect(*args, **kwargs):
"""Side effect to ensure FASTXValidator gets properly read
Expand Down

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