UCSD Oasis platform

Related tags

Deep Learning oasis
Overview

oasis

Build Status

UCSD Oasis platform

Local project setup

  1. Install Docker Compose and make sure you have Pip installed
  2. Clone the project and go to the project folder in your console
  3. Run ./dev-setup to build the project
    • Tip: Make sure to run this command regularly, or at least, every time you start something fresh from master!
  4. To run the app: docker-compose up - navigate to http://localhost:3000 to see it! 🚀
    • All API endpoints are available in http://localhost:8000/api/{endpoint-name-here}

Adding packages to the frontend

If you need to add packages to the frontend app, make sure to do so with yarn and within the docker environment:

docker-compose run --rm ui yarn add PACKAGE_NAME_HERE 

Creating new backend apps with models

If you're creating an app on the backend and it contains models, you'll need to set up a couple of things to make sure migrations work. To begin with, in your app's models.py make sure to import the app's declarative base and creating your models based off that:

from database import Base

class YourCoolModel(Base):
    __tablename__ = "super_cool_models"
    id = Column(Integer, primary_key=True, index=True)
    # all your cool model attributes go here

After that, head over to alembic.env and import your models on the top section of the file:

from users import models
from yourcoolapp import models

That's about it! Migrations should auto-generate correctly with that set up!

Generating & running migrations

As part of our everyday work, data models may change from time to time. When you change a model in the backend, make sure to run the following code to generate any necessary Alembic migrations:

docker-compose run --rm api alembic revision --autogenerate -m "Migration name here!"

When possible, keep the migration name descriptive!

When a new migration file is available, apply it by running

./dev-setup.sh

If you want to run them manually you can also do:

docker-compose run --rm api alembic upgrade head

You can also roll back migrations by doing

docker-compose run --rm api alembic downgrade -1

Seeding data

To populate development database with seed data, which is located in /backend/almebic/seed_data directory, run:

docker-compose run --rm api python alembic/seed.py

To add seed data or modify existing one, apply changes in <entity>.json file for the target entity in aforementioned /backend/alembic/seed_data directory. Make sure that the script uses the data you are interested in, by checking the "files to be imported" at the top of the script.

Running backend tests

All tests for the backed are within the /backend/tests folder, and they're run automatically on branches and PRs by Travis. You can run them by doing:

docker-compose run --rm -e DATABASE_NAME='dbtest' api pytest

Building & deploying

Builds are generated automatically whenever we:

  • Push to master (updates the dev image)
  • Push to a branch named release/something (updates an image called release/something-dev)
  • Tag the project (generates a tag-name image)

After doing any of these actions, you can head over to Travis to see how the build is faring.

With the build ready, head over to Rancher to upgrade the Oasis instances in the environment you need to deploy to.

Make sure to:

  1. first upgrade the db-migration container if there is any new migration,
  2. then the app container adding any necessary environment variables
Comments
  • Git commit failed after creating new db model.

    Git commit failed after creating new db model.

    I followed the steps in README.md to create a new model for persisting my story. But seems like I'm failing some of the pre-commit stages that prevent me from committing and pushing. The log is as followed:

    16:51 Commit failed with error 0 files committed, 6 files failed to commit: Add my_story table black....................................................................Passed flake8...................................................................Failed - hook id: flake8 - exit code: 1 backend/alembic/env.py:8:1: F401 'stories.models as story_models' imported but unused backend/alembic/env.py:9:1: F401 'users.models as user_models' imported but unused backend/alembic/env.py:10:1: F401 'mystories.models as mystory_models' imported but unused prettier.................................................................Passed

    It seems like the lines for importing new models in /backend/alembic/env.py are marked as unused import statements. Can someone give me some pointers how to circumvent this? Thanks!

    image

    help wanted question 
    opened by vinovo 9
  • Error after clicking next on the CriticalQuestions page

    Error after clicking next on the CriticalQuestions page

    Based on master(common issue):

    Error: Objects are not valid as a React child (found: object with keys {loc, msg, type}). If you meant to render a collection of children, use an array instead.
        in p (at CriticalQuestions/index.js:212)
        in CriticalQuestions (created by Context.Consumer)
        in Route (at src/index.js:39)
        in Switch (at src/index.js:34)
        in div (at Wrapper/index.js:22)
        in main (at Wrapper/index.js:20)
        in Wrapper (at src/index.js:33)
        in Router (at src/index.js:29)
        in MuiPickersUtilsProvider (at src/index.js:28)
        in Provider (at src/index.js:27)
    
    good first issue 
    opened by yus252 8
  • Feature/108 change status

    Feature/108 change status

    Added a SickCheck and TestCheck page that's similar to Onboard and Confirm respectively to allow daily assessment to update sick and test status without going to the critical questions page and only go to symptoms page if sick is selected.

    opened by yxlin118 6
  • Add story marker

    Add story marker

    The map should show the user all the stories (saved in Story table in database). Need to:

    • [x] Get all the my_stories and corresponding info, such as gender, sex, sick, tested and so on from Story table. (Database)
    • [x] Get the coordinate of the city's center + a random distance from the center of the city(Mapbox Reverse Geocoding)
    • [x] Add a marker for each story with the text to the map(Mapbox Marker)
    • [x] Style the story popups.
    enhancement epic 
    opened by yus252 4
  • Exposure notification

    Exposure notification

    Functionality

    When a user submits close contacts, if the user is sick 🤒 and tested positive 🧪 the application sends exposure notification email to the corresponding email addresses The above is done on background to prevent blocking the site

    Email notifications ✉️

    If a user-contact was notified in the last 4 days, no email is sent (to avoid spamming) If a user-contact was notified, but more than 4 days ago, then a new email is sent All new email addresses are notified

    In all the above cases, the application stores the association between the email address and the story that is reporting the relation (whether the email was sent or not). This is to be able to:

    • keep track of the amount of mails where sent based on a story (it may not be the same as the current story close-contacts since can be updated)
    • know how many sick people a person (email address) was exposed to

    Environments 🔩

    • The application depends on the SMTP_ environment variables to be present in all the environments that are not dev
    • In dev environment, emails are not sent but printed in stdoud and no further configuration is needed

    Implementation 👀

    email-sender implementation is from aws ses documentation

    closes #3

    opened by anaPerezGhiglia 4
  • Cannot Sign In Locally

    Cannot Sign In Locally

    Based on master(backend issue): After showing "We're checking your credentials...", it does not jump to the map/story page or show any error message.

    opened by yus252 4
  • Add map legend

    Add map legend

    Map legend 🗺️

    • All the data is now being clustered in 5 groups
    • values are rounded to the three-most-significant digit
    • values are only rounded in the legend Rounded breaks are not used for clustering the data, since it can happen that the rounded upper limit < some regions cases. If this happens, it would end in those regions not being member of any cluster. For example, if a region has 2,163,543 active cases, the rounded limit would be 2,160,000. Thus, if clustering with such upper-limit would end with such region out of the cluster

    UI tweaks 🔩

    For showing the legend alongside all the data that was already being displayed without having overlapping, some rearrangements where needed:

    • New wording latest totals
    • New wording actives
    • New layout for showing latestUpdate
    • Smaller status dot size 🔴
    • Add toLocaleString() to numbers (#100)
    • Rearrange of suggestions, latestUpdate and userStatus order

    Mobile

    Desktop

    Bonus ➕

    • remove unnecessary docker-compose up db from dev-setup.sh

    closes #94

    opened by anaPerezGhiglia 4
  • Add map legend on <Dashboard />

    Add map legend on

    • [x] Implement the default mapbox legend on the bottom left corner of the <Dashboard/>
      • maybe make it dependant on the draggable prop? maybe add a displayLegend prop that's set by the <Wrapper/>? have fun!
    • [x] Integrate visually suggestions box with my status
      • remove "my status" title & inline the two existing lines
    • [x] display "latest update" below suggestions & status
    • [x] reduce spacing around titles for these boxes (at least on mobile)
    opened by pyritewolf 4
  • Get user actions based on status

    Get user actions based on status

    • [ ] generate an endpoint on the backend that, based on a user's status (sick / not sick, tested / not tested, etc) returns different resources to be displayed in the frontend
      • This still needs some design as to what actionable items are needed on each set of conditions
    • [ ] Use that to display actionable items to the user once they're onboarded
    opened by pyritewolf 4
  • Save Story information lifted from onboarding

    Save Story information lifted from onboarding

    Bear in mind, this data model is tentative! If you think something could be improved, do share any ideas.

    • [ ] Add new Story model, linked 1-to-1 to Users (optional FK):
      • age: integer
      • sex: "male" | "female" | "other"
      • ethnicity: string
      • countryOfOrigin: string
      • profession: string
      • medicalProblems: format tbd, it's a short list of texts - possibly an auxiliary table?
      • isSick: "not_sick" | "sick" | "recovered"
      • isTested: "positive" | "negative" | "not_tested"
    • [ ] Hook frontend so that all this information (collected during user onboarding) is stored in the backend with the POST endpoint
    opened by pyritewolf 4
  • Exposure notification (anonymous)

    Exposure notification (anonymous)

    After a C+ reports to have been in contact with someone, trigger an anonymous email to that person with the following text:

    `Dear FirstName, this is a notice informing that you have been may have been exposed to individuals (contacts) infected with the COVID-19 virus

    Please go to myoasis.ucsd.edu for more information and to report how you are feeling. You are encouraged to stay home and maintain social distance from others (at least 6 feet) until 14 days after your last exposure, in case you also become ill.

    You should monitor yourself by checking your temperature twice daily and watching for cough or shortness of breath.

    If you develop symptoms you should promptly isolate yourself and notify your doctor or public health staff.

    You should be promptly evaluated for infection and for the need for medical care. You can learn more about how to care for yourself if you’ve been exposed here: link https://www.sandiegocounty.gov/content/dam/sdc/hhsa/programs/phs/Epidemiology/COVID-19%20Home%20Quarantine%20Guidance.pdf https://www.cdc.gov/coronavirus/2019-ncov/php/public-health-recommendations.html `

    opened by nditada 4
  • Bump express from 4.17.1 to 4.18.2 in /frontend

    Bump express from 4.17.1 to 4.18.2 in /frontend

    Bumps express from 4.17.1 to 4.18.2.

    Release notes

    Sourced from express's releases.

    4.18.2

    4.18.1

    • Fix hanging on large stack of sync routes

    4.18.0

    ... (truncated)

    Changelog

    Sourced from express's changelog.

    4.18.2 / 2022-10-08

    4.18.1 / 2022-04-29

    • Fix hanging on large stack of sync routes

    4.18.0 / 2022-04-25

    ... (truncated)

    Commits

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    dependencies javascript 
    opened by dependabot[bot] 0
  • Bump qs from 6.5.2 to 6.5.3 in /frontend

    Bump qs from 6.5.2 to 6.5.3 in /frontend

    Bumps qs from 6.5.2 to 6.5.3.

    Changelog

    Sourced from qs's changelog.

    6.5.3

    • [Fix] parse: ignore __proto__ keys (#428)
    • [Fix] utils.merge: avoid a crash with a null target and a truthy non-array source
    • [Fix] correctly parse nested arrays
    • [Fix] stringify: fix a crash with strictNullHandling and a custom filter/serializeDate (#279)
    • [Fix] utils: merge: fix crash when source is a truthy primitive & no options are provided
    • [Fix] when parseArrays is false, properly handle keys ending in []
    • [Fix] fix for an impossible situation: when the formatter is called with a non-string value
    • [Fix] utils.merge: avoid a crash with a null target and an array source
    • [Refactor] utils: reduce observable [[Get]]s
    • [Refactor] use cached Array.isArray
    • [Refactor] stringify: Avoid arr = arr.concat(...), push to the existing instance (#269)
    • [Refactor] parse: only need to reassign the var once
    • [Robustness] stringify: avoid relying on a global undefined (#427)
    • [readme] remove travis badge; add github actions/codecov badges; update URLs
    • [Docs] Clean up license text so it’s properly detected as BSD-3-Clause
    • [Docs] Clarify the need for "arrayLimit" option
    • [meta] fix README.md (#399)
    • [meta] add FUNDING.yml
    • [actions] backport actions from main
    • [Tests] always use String(x) over x.toString()
    • [Tests] remove nonexistent tape option
    • [Dev Deps] backport from main
    Commits
    • 298bfa5 v6.5.3
    • ed0f5dc [Fix] parse: ignore __proto__ keys (#428)
    • 691e739 [Robustness] stringify: avoid relying on a global undefined (#427)
    • 1072d57 [readme] remove travis badge; add github actions/codecov badges; update URLs
    • 12ac1c4 [meta] fix README.md (#399)
    • 0338716 [actions] backport actions from main
    • 5639c20 Clean up license text so it’s properly detected as BSD-3-Clause
    • 51b8a0b add FUNDING.yml
    • 45f6759 [Fix] fix for an impossible situation: when the formatter is called with a no...
    • f814a7f [Dev Deps] backport from main
    • Additional commits viewable in compare view

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    dependencies javascript 
    opened by dependabot[bot] 0
  • Bump decode-uri-component from 0.2.0 to 0.2.2 in /frontend

    Bump decode-uri-component from 0.2.0 to 0.2.2 in /frontend

    Bumps decode-uri-component from 0.2.0 to 0.2.2.

    Release notes

    Sourced from decode-uri-component's releases.

    v0.2.2

    • Prevent overwriting previously decoded tokens 980e0bf

    https://github.com/SamVerschueren/decode-uri-component/compare/v0.2.1...v0.2.2

    v0.2.1

    • Switch to GitHub workflows 76abc93
    • Fix issue where decode throws - fixes #6 746ca5d
    • Update license (#1) 486d7e2
    • Tidelift tasks a650457
    • Meta tweaks 66e1c28

    https://github.com/SamVerschueren/decode-uri-component/compare/v0.2.0...v0.2.1

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    dependencies javascript 
    opened by dependabot[bot] 0
  • Bump terser from 4.6.7 to 4.8.1 in /frontend

    Bump terser from 4.6.7 to 4.8.1 in /frontend

    Bumps terser from 4.6.7 to 4.8.1.

    Changelog

    Sourced from terser's changelog.

    v4.8.1 (backport)

    • Security fix for RegExps that should not be evaluated (regexp DDOS)

    v4.8.0

    • Support for numeric separators (million = 1_000_000) was added.
    • Assigning properties to a class is now assumed to be pure.
    • Fixed bug where yield wasn't considered a valid property key in generators.

    v4.7.0

    • A bug was fixed where an arrow function would have the wrong size
    • arguments object is now considered safe to retrieve properties from (useful for length, or 0) even when pure_getters is not set.
    • Fixed erroneous const declarations without value (which is invalid) in some corner cases when using collapse_vars.

    v4.6.13

    • Fixed issue where ES5 object properties were being turned into ES6 object properties due to more lax unicode rules.
    • Fixed parsing of BigInt with lowercase e in them.

    v4.6.12

    • Fixed subtree comparison code, making it see that [1,[2, 3]] is different from [1, 2, [3]]
    • Printing of unicode identifiers has been improved

    v4.6.11

    • Read unused classes' properties and method keys, to figure out if they use other variables.
    • Prevent inlining into block scopes when there are name collisions
    • Functions are no longer inlined into parameter defaults, because they live in their own special scope.
    • When inlining identity functions, take into account the fact they may be used to drop this in function calls.
    • Nullish coalescing operator (x ?? y), plus basic optimization for it.
    • Template literals in binary expressions such as + have been further optimized

    v4.6.10

    • Do not use reduce_vars when classes are present

    v4.6.9

    • Check if block scopes actually exist in blocks

    v4.6.8

    • Take into account "executed bits" of classes like static properties or computed keys, when checking if a class evaluation might throw or have side effects.
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    dependencies javascript 
    opened by dependabot[bot] 0
  • Bump moment from 2.25.3 to 2.29.4 in /frontend

    Bump moment from 2.25.3 to 2.29.4 in /frontend

    Bumps moment from 2.25.3 to 2.29.4.

    Changelog

    Sourced from moment's changelog.

    2.29.4

    • Release Jul 6, 2022
      • #6015 [bugfix] Fix ReDoS in preprocessRFC2822 regex

    2.29.3 Full changelog

    • Release Apr 17, 2022
      • #5995 [bugfix] Remove const usage
      • #5990 misc: fix advisory link

    2.29.2 See full changelog

    • Release Apr 3 2022

    Address https://github.com/moment/moment/security/advisories/GHSA-8hfj-j24r-96c4

    2.29.1 See full changelog

    • Release Oct 6, 2020

    Updated deprecation message, bugfix in hi locale

    2.29.0 See full changelog

    • Release Sept 22, 2020

    New locales (es-mx, bn-bd). Minor bugfixes and locale improvements. More tests. Moment is in maintenance mode. Read more at this link: https://momentjs.com/docs/#/-project-status/

    2.28.0 See full changelog

    • Release Sept 13, 2020

    Fix bug where .format() modifies original instance, and locale updates

    2.27.0 See full changelog

    • Release June 18, 2020

    Added Turkmen locale, other locale improvements, slight TypeScript fixes

    2.26.0 See full changelog

    • Release May 19, 2020

    ... (truncated)

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    dependencies javascript 
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  • Bump eventsource from 1.0.7 to 1.1.1 in /frontend

    Bump eventsource from 1.0.7 to 1.1.1 in /frontend

    Bumps eventsource from 1.0.7 to 1.1.1.

    Changelog

    Sourced from eventsource's changelog.

    1.1.1

    • Do not include authorization and cookie headers on redirect to different origin (#273 Espen Hovlandsdal)

    1.1.0

    • Improve performance for large messages across many chunks (#130 Trent Willis)
    • Add createConnection option for http or https requests (#120 Vasily Lavrov)
    • Support HTTP 302 redirects (#116 Ryan Bonte)
    • Prevent sequential errors from attempting multiple reconnections (#125 David Patty)
    • Add new to correct test (#111 Stéphane Alnet)
    • Fix reconnections attempts now happen more than once (#136 Icy Fish)
    Commits
    • aa7a408 1.1.1
    • 56d489e chore: rebuild polyfill
    • 4a951e5 docs: update history for 1.1.1
    • f9f6416 fix: strip sensitive headers on redirect to different origin
    • 9dd0687 1.1.0
    • 49497ba Update history for 1.1.0 (#146)
    • 3a38537 Update history for #136
    • 46fe04e Merge pull request #136 from icy-fish/master
    • 9a4190f Fix issue: reconnection only happends for 1 time after connection drops
    • 61e1b19 test: destroy both proxied request and response on close
    • Additional commits viewable in compare view

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  • v1.0.0(Jul 7, 2020)

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