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Add AWS credentials to vault (#220)
* Fix test affected by backfill * Set target python version * Update: added new use case in safegraph * change in params.json.template * update in params.json.template: wip_prefix to wip_signal * Changed func name from epidata_signal() -- > public_signal(), signal_name() --> add_prefix() for better readability * cleaner code, * handling wip signal in python template * Minor changes in process.py, updated test cases * signal naming using wip_signal parameter * Supply missing params.json.template in tests * Switch from raw Epidata client to COVIDcast client * Move signal name constants to their own file, referenced from both run.py and process.py * Corrected logic to comply with #113 * Also converted unit test to test the process.py logic instead of the validity of the params file. * Corrected errors I'd introduced in the conversion to covidcast client * changes in compliance with #205 * Missing comma in setup.py * Linter suggested changes, added HOME_DWELL signal computation * changes in compliance with #205 * default prefix value * Apply suggestions from code review Co-authored-by: krivard <[email protected]> * Removed unnecessary comment * Updated constants.py * Updated README.md * Updated update_sensor.py * updated params.json.template * updated tests/params.json.template * New test case file for handling wip signal * Updated test_update_sensor.py * Update constants.py * Update update_sensor.py * Update test_update_sensor.py * Update test_update_sensor.py * Update update_sensor.py * Update update_sensor.py * Set up initial google_health-deploy branch - Add new google_health Jenkins pipeline stage scripts - Add the abilty for Ansible to write either a file or a template depending on which has been configured for the indicator - Add Ansible template directory (special tall bookshelf) - Add the ability to keep sensitive variables in `vault.yaml` - Add google_health production params template Encrypt vault.yaml - Use templates dir - Configure start_date and end_date * Finalize production config for google_health deployment (#165) * Switch to midas export dir * Properly rename Jenkins pipeline stage scripts * Handle google_health's testing needs - Add: Ansible playbook for securely handling placing the `params.json` template we need for testing. This will happen during the Jenkins build stage when we are setting up the venv in the workspace on the Jenkins server. - Add: Test `params.json` template. - Add: Jenkins user variable. - Fix: Was incorrectly trying to use a file instead of a template in `ansible-deploy.yaml`. - Add: Call the small Ansible playbook from the Jenkins build wrapper. * Change to the Ansible root dir before trying to do Ansible things * Delegate to localhost * Tell Ansible we want to connect locally for this playbook * Remove set -x from Bash scripts * used set instead of list to compare dict.keys() (#186) Co-authored-by: Vishakha Srivastava <[email protected]> * Use brace instead of bracket (#189) * Add path parameter (#190) * Allow `""` for `start_date` to get "latest" data (#194) - We can treat this like we do `end_date` and default to a date to some number of days in the past. The result is that we only process updates for one day, instead of of the whole shebang. - Add new cache files, a temporary necessity. * Set start date to empty string (#203) * Add a cache set that this identical to production (#211) * Sync cache * Remove end date from params * Add AWS credentials to vault Co-authored-by: Chua Eu Jing <[email protected]> Co-authored-by: Vishakha <[email protected]> Co-authored-by: Kathryn M Mazaitis <[email protected]> Co-authored-by: Addison Hu <[email protected]>
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‎_template_python/delphi_NAME/constants.py

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"""
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Registry for signal names
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"""
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## example:
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# FULL_TIME = "full_time_work_prop"
8+
# PART_TIME = "part_time_work_prop"
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# COVIDNET = "covidnet"
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#
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# SIGNALS = [
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# FULL_TIME,
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# PART_TIME,
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# COVIDNET
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# ]
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SIGNALS = []

‎_template_python/delphi_NAME/handle_wip_signal.py

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"""
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Handle signal names.
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Author: Vishakha
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Created: 2020-08-07
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"""
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import covidcast
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def add_prefix(signal_names, wip_signal, prefix="wip_"):
12+
"""Adds prefix to signal if there is a WIP signal
13+
Parameters
14+
----------
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signal_names: List[str]
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Names of signals to be exported
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prefix : 'wip_'
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prefix for new/non public signals
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wip_signal : List[str] or bool
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a list of wip signals: [], OR
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all signals in the registry: True OR
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only signals that have never been published: False
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Returns
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-------
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List of signal names
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wip/non wip signals for further computation
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"""
28+
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if wip_signal is True:
30+
return [prefix + signal for signal in signal_names]
31+
if isinstance(wip_signal, list):
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make_wip = set(wip_signal)
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return[
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prefix + signal if signal in make_wip else signal
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for signal in signal_names
36+
]
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if wip_signal in {False, ""}:
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return [
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signal if public_signal(signal)
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else prefix + signal
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for signal in signal_names
42+
]
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raise ValueError("Supply True | False or '' or [] | list()")
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def public_signal(signal_):
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"""Checks if the signal name is already public using COVIDcast
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Parameters
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----------
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signal_ : str
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Name of the signal
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Returns
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-------
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bool
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True if the signal is present
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False if the signal is not present
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"""
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epidata_df = covidcast.metadata()
59+
for index in range(len(epidata_df)):
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if epidata_df['signal'][index] == signal_:
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return True
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return False

‎_template_python/delphi_NAME/run.py

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This module should contain a function called `run_module`, that is executed
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when the module is run with `python -m MODULE_NAME`.
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"""
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import numpy as np
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import pandas as pd
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from delphi_utils import read_params
10-
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from .handle_wip_signal import add_prefix
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from .constants import SIGNALS
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def run_module():
13-
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"""
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Calls the method for handling the wip signals
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Returns
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-------
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prints the updated signal names
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"""
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params = read_params()
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wip_signal = params["wip_signal"]
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signal_names = add_prefix(SIGNALS, wip_signal, prefix="wip_")
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print(signal_names)

‎_template_python/params.json.template

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{
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"static_file_dir": "./static",
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"export_dir": "./receiving",
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"cache_dir": "./cache"
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"cache_dir": "./cache",
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"wip_signal": ""
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}

‎_template_python/setup.py

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"pytest",
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"pytest-cov",
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"pylint",
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"delphi-utils"
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"delphi-utils",
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"covidcast"
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]
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setup(

‎_template_python/tests/params.json.template

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{
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"static_file_dir": "../static",
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"export_dir": "./receiving",
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"cache_dir": "./cache"
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"cache_dir": "./cache",
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"wip_signal": ""
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}

‎_template_python/tests/test_handle_wip_signal.py

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import unittest
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from delphi_NAME.handle_wip_signal import add_prefix
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from delphi_NAME.run import SIGNALS
4+
from delphi_utils import read_params
5+
6+
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8+
def test_handle_wip_signal():
9+
# Test wip_signal = True (all signals should receive prefix)
10+
signal_names = add_prefix(SIGNALS, True, prefix="wip_")
11+
assert all(s.startswith("wip_") for s in signal_names)
12+
# Test wip_signal = list (only listed signals should receive prefix)
13+
signal_names = add_prefix(SIGNALS, [SIGNALS[0]], prefix="wip_")
14+
assert signal_names[0].startswith("wip_")
15+
assert all(not s.startswith("wip_") for s in signal_names[1:])
16+
# Test wip_signal = False (only unpublished signals should receive prefix)
17+
signal_names = add_prefix(["xyzzy", SIGNALS[0]], False, prefix="wip_")
18+
assert signal_names[0].startswith("wip_")
19+
assert all(not s.startswith("wip_") for s in signal_names[1:])
20+
21+
22+
class MyTestCase(unittest.TestCase):
23+
pass
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if __name__ == '__main__':
27+
unittest.main()

‎ansible/google_health-build.yaml

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---
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- hosts: localhost
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connection: local
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vars_files:
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- vars.yaml
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- vault.yaml
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tasks:
8+
- name: Set test params template.
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template:
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src: templates/{{ indicator }}-params-test.json.j2
11+
dest: "{{ workspace }}/{{ indicator }}/tests/params.json"
12+
owner: "{{ jenkins_user }}"
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group: "{{ jenkins_user }}"
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mode: "0644"
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delegate_to: localhost

‎ansible/templates/google_health-params-prod.json.j2

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{
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"static_file_dir": "./static",
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"export_dir": "/common/covidcast/receiving/ght",
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"cache_dir": "./cache",
5+
"start_date": "",
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"end_date": "",
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"ght_key": "{{ google_health_api_key }}"
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}

‎ansible/templates/google_health-params-test.json.j2

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{
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"static_file_dir": "../static",
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"export_dir": "./receiving",
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"cache_dir": "../cache",
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"start_date": "2020-02-11",
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"end_date": "2020-04-30",
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"ght_key": "{{ google_health_api_key }}"
8+
}

‎ansible/vars.yaml

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---
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runtime_user: "indicators"
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jenkins_user: "jenkins"
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jenkins_artifact_dir: "/var/lib/jenkins/artifacts"
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indicators_runtime_dir: "/home/{{ runtime_user }}/runtime"
5-
package: "{{ indicator }}.tar.gz" # This is passed in the Ansible invocation.
6+
package: "{{ indicator }}.tar.gz" # {{ indicator }} is passed in from the Jenkins shell script wrapper.
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python_version: "3.8.2"
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pyenv_python_path: "/home/{{ runtime_user }}/.pyenv/versions/{{ python_version }}/bin/python"
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# Indicators variables.
11+
google_health_api_key: "{{ vault_google_health_api_key }}"
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delphi_aws_access_key_id: "{{ vault_delphi_aws_access_key_id }}"
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delphi_aws_secret_access_key: "{{ vault_delphi_aws_secret_access_key }}"

‎ansible/vault.yaml

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$ANSIBLE_VAULT;1.1;AES256
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66386163643862646634343162646465663762643034303563333833633661333932646164656462
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6166646131623132393238336263623562373065643633310a663232373237396361623462613333
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62373663383565623263306539636431623230633065626363666531366662363065343066363031
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3738616663336665340a326138333634306137363837396366303861663064326333613662656630
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62306331646637326637363766366237663037306665343761643263646663316535343561623137
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63313365653535393639626465343232396261643239303430383138633135346466323834336665
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33633064353034613836313265613466623961373565363835343430373138376336363966316365
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35663664396436313432376264316663326130306134326231303234393561643436623039613136
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63366638396262383762383336643930343661636461646162653734336334306239383132643435
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39333665643738643966356431333830646561353263353063326330643731616130396466343339
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39346437653063303336626663623835613938633834396430353634383366386237353862643766
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37393738353231666565303031393839306463373461393761653866653330646534393832303264
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30323038646166366465396235623731343539313633326539663966333437623733626131653437
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62326632656462383835656235373664366566343866383938343639613737623631616231616135
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633863383761366461363532353137323936

‎cdc_covidnet/README.md

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Unit tests are also included in the module. To execute these, run the following
5656
command from this directory:
57-
57+
(Note: the following command requires python 3.8, having any version less than 3.8 might
58+
fail some test cases. Please install it before running.)
5859
```
5960
(cd tests && ../env/bin/pytest --cov=delphi_cdc_covidnet --cov-report=term-missing)
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```

‎cdc_covidnet/delphi_cdc_covidnet/constants.py

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"""
2+
Registry for signal names
3+
"""
4+
COVIDNET = "covidnet"
5+
SIGNALS = [COVIDNET]

‎cdc_covidnet/delphi_cdc_covidnet/covidnet.py

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134134
for nid, cid in args.itertuples(index=False, name=None):
135135
outfile = os.path.join(cache_path, f"networkid_{nid}_catchmentid_{cid}.json")
136136
state_files.append(outfile)
137-
args = (nid, cid, age_groups, APIConfig.SEASONS, outfile, APIConfig.HOSP_URL)
138-
state_args.append(args)
137+
if not os.path.exists(outfile):
138+
args = (nid, cid, age_groups, APIConfig.SEASONS, outfile, APIConfig.HOSP_URL)
139+
state_args.append(args)
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140141
# Download all state files
141142
if parallel:

‎cdc_covidnet/delphi_cdc_covidnet/run.py

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"""
77
import logging
88
from datetime import datetime
9+
from os import remove
910
from os.path import join
1011

1112
from delphi_utils import read_params
@@ -57,4 +58,9 @@ def run_module():
5758
start_date,
5859
end_date)
5960

61+
# Cleanup cache dir
62+
remove(mappings_file)
63+
for state_file in state_files:
64+
remove(state_file)
65+
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logging.info("finished all")

‎cdc_covidnet/delphi_cdc_covidnet/update_sensor.py

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import numpy as np
1313
import pandas as pd
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15+
from delphi_utils import read_params
16+
import covidcast
1517
from .api_config import APIConfig
1618
from .covidnet import CovidNet
1719
from .geo_maps import GeoMaps
20+
from .constants import SIGNALS
1821

1922
def write_to_csv(data: pd.DataFrame, out_name: str, output_path: str):
2023
"""
@@ -93,7 +96,62 @@ def update_sensor(
9396
hosp_df["sample_size"] = np.nan
9497

9598
# Write results
96-
out_name = "wip_covidnet"
97-
write_to_csv(hosp_df, out_name, output_path)
99+
signals = add_prefix(SIGNALS, wip_signal=read_params()["wip_signal"], prefix="wip_")
100+
for signal in signals:
101+
write_to_csv(hosp_df, signal, output_path)
98102

99103
return hosp_df
104+
105+
106+
def add_prefix(signal_names, wip_signal, prefix):
107+
"""Adds prefix to signal if there is a WIP signal
108+
Parameters
109+
----------
110+
signal_names: List[str]
111+
Names of signals to be exported
112+
prefix : 'wip_'
113+
prefix for new/non public signals
114+
wip_signal : List[str] or bool
115+
a list of wip signals: [], OR
116+
all signals in the registry: True OR
117+
only signals that have never been published: False
118+
Returns
119+
-------
120+
List of signal names
121+
wip/non wip signals for further computation
122+
"""
123+
124+
if wip_signal is True:
125+
return [prefix + signal for signal in signal_names]
126+
if isinstance(wip_signal, list):
127+
make_wip = set(wip_signal)
128+
return [
129+
(prefix if signal in make_wip else "") + signal
130+
for signal in signal_names
131+
]
132+
if wip_signal in {False, ""}:
133+
return [
134+
signal if public_signal(signal)
135+
else prefix + signal
136+
for signal in signal_names
137+
]
138+
raise ValueError("Supply True | False or '' or [] | list()")
139+
140+
141+
def public_signal(signal_):
142+
"""Checks if the signal name is already public using COVIDcast
143+
Parameters
144+
----------
145+
signal_ : str
146+
Name of the signal
147+
Returns
148+
-------
149+
bool
150+
True if the signal is present
151+
False if the signal is not present
152+
"""
153+
epidata_df = covidcast.metadata()
154+
for index in range(len(epidata_df)):
155+
if epidata_df['signal'][index] == signal_:
156+
return True
157+
return False

‎cdc_covidnet/params.json.template

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"cache_dir": "./cache",
55
"start_date": "2020-03-07",
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"end_date": "",
7-
"parallel": false
7+
"parallel": false,
8+
"wip_signal": ""
89
}

‎cdc_covidnet/setup.py

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"pytest-cov",
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"pylint",
1010
"delphi-utils",
11-
"requests"
11+
"requests",
12+
"covidcast"
1213
]
1314

1415
setup(
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2223
classifiers=[
2324
"Development Status :: 5 - Production/Stable",
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"Intended Audience :: Developers",
25-
"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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],
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packages=find_packages(),
2829
)

‎cdc_covidnet/tests/cache_test/init.json

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‎cdc_covidnet/tests/cache_test/networkid_2_catchmentid_1.json

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{"datadownload": [{"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "10", "age_category": "Overall", "cumulative-rate": 0.2, "weekly-rate": 0.2}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "11", "age_category": "Overall", "cumulative-rate": 1, "weekly-rate": 0.8}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "12", "age_category": "Overall", "cumulative-rate": 3.2, "weekly-rate": 2.2}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "13", "age_category": "Overall", "cumulative-rate": 6.8, "weekly-rate": 3.6}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "14", "age_category": "Overall", "cumulative-rate": 10.8, "weekly-rate": 3.9}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "15", "age_category": "Overall", "cumulative-rate": 14.7, "weekly-rate": 3.9}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "16", "age_category": "Overall", "cumulative-rate": 17.8, "weekly-rate": 3.1}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "17", "age_category": "Overall", "cumulative-rate": 20, "weekly-rate": 2.2}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "18", "age_category": "Overall", "cumulative-rate": 22.5, "weekly-rate": 2.5}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "19", "age_category": "Overall", "cumulative-rate": 25, "weekly-rate": 2.5}, {"catchment": "California", "network": "EIP", "year": "2020", "mmwr-year": "2020", "mmwr-week": "20", "age_category": "Overall", "cumulative-rate": 27, "weekly-rate": 2}, {"catchment": "California", "network": "EIP", "year": 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