portal-backend

Check out the ansible configs repo (https://stash.broadinstitute.org/projects/CPDS/repos/ansible-configs/browse) at the same directory level as where the depmap repo is checked out. It contains a download key used for building the dev database and accessing downloads.

Also set up your taiga token (https://cds.team/taiga/token/)

Create a virtual environment, install Python and Javascript dependencies:

./install_prereqs.sh

Create and populate the database :

# first, in a different window, start breadbox, redis and the worker process
cd ../breadbox
./bb run &
redis-server &
./bb run_worker &

# then back in portal-backend create empty DB and sync the data into breadbox
./flask recreate_dev_db

In one window, compile the Javascript :

./flask webpack

In another window, start breadbox. For this follow the instructions in breadbox/README.md

Finally, in another window, run the app :

./flask run

At this point, the portal should be running locally.

If you use part of the website which requires a background worker (e.g. custom associations) you also need to start Redis which is used to hold results and as the message broker, and start the celery worker process :

redis-server
./flask run_dev_worker

Shell

To open the interactive shell, run :

./flask shell

You have access to the flask app variable, and variables listed in app.py -> register_shellcontext -> shell_context.

Running Tests

To run all backend tests, run :

pytest

Examples of running specific tests: :

pytest <path/to/test/file.py>::<name_of_test_method>
pytest tests/depmap/context/test_models.py::test_get_entities_enriched_in_context_query

pytest -k <name of test>
pytest -k test_get_entities_enriched_in_context_query

To open a debugger shell on test failure, run pytest with the \--pdb option

To run all frontend tests:

cd frontend
yarn test

To run tests in a specific file:

yarn test controlledPlot --passWithNoTests

(The --passWithNoTests flag is being used here because we're running tests on all packages and most of them will not produce any matches for "controlledPlot." This is not need if you cd into that specific package first.)

To further run only one test in the file, provide part of the test name to match on to the -t option :

cd frontend/packages/\@depmap/interactive
yarn test controlledPlot -t "partial name of test"

it('partial name of test that does stuff', () => {
});

Writing Tests

All non-trivial code backend should have a corresponding test, except for code in the (which is not tested). Frontend code testing is nice but not required.

Launching Storybook

We use storybook to help develop react components in isolation. To run storybook, run:

cd frontend/packages/portal-frontend
yarn storybook

Global css and js can be added to portal_frontend/.storybook/preview-head.html

To instantiate a component with a set of props on storybook, create a/edit the <ComponentName>.stories.tsx file in the same directory location as <ComponentName>.tsx

Directory structure

The directory structure of the tests directory should mirror that of the depmap directory. E.g., functions in depmap/cell_line/views.py should have their test in tests/depmap/cell_line/test_views.py. If there are many tests for functions within one file, the name of the file been tested may be a directory instead, e.g. tests/depmap/interactive/views has files named after the tested functions.

Populating db objects

We have factories defined in tests/factories.py to help set up database objects necessary for a test, see examples in tests/depmap/dataset/test_models.py. Some older tests use fixtures like populated_db, this method is deprecated in favor of starting from an empty database and using factories.

Overriding the flask config

See tests/depmap/vector_catalog/nodes/continuous_tree/test_dataset_sort_key.py for an example.

Development Conventions

Recreating dev db

./flask recreate_dev_db by default skips loading entirety of non-core portions of the portal (nonstandard, celligner, tda, and constellation). For constellation, sample data is loaded, while the others are completely skipped. :

./flask recreate_dev_db

To load those, add their respective flags (-n, -c, -t, and -d). :

./flask recreate_dev_db -nctd

Testing locally with non-dev data

There are bash scripts under the /portal-backend directory which copy data from specific environments and update values in portal-backend/flask to simulate the non-dev environment locally.

For example, copy-data-from-iqa.sh rebuilds the database with iqa data (and takes 5-10 minutes to run).

Representative full-feature examples

Sample data has many holes, but we want at least one gene, one compound, and one cell line that has all data for all features, so that we can get an idea of what the page looks like with all features/colors etc. If adding a new feature to the gene/compound/cell line page, ensure that sample data for the representative gene/compound

Gene: SOX10

Compound: afatinib

Cell line: UACC62 ( ACH-000425 )

These are also marked in the sample_data/subsets.py file, which enumerates the genes, compounds, and cell lines in the dev database.

Likewise, we have a single private dataset named "Canary dataset" which only users "[email protected]", "<anything>@canary.com" or "<anything>@canary.org" are allowed to see. See "Testing with private data" to see details for how to test viewing private data.

URL Conventions

All the url routes should separate the words with an underscore (\_) and lower case. For example: The URL to Cell STRAINER would be {basename}/cell_strainer

Model Conventions:

DB tables are singular, lower case using underscores between words, consistent with class name.

Subsetting sample data:

Genes, compounds, and cell lines used are in sample_data/subset_files/subsets.py

Code style:

We use black (python) and prettier (javascript) code formatters to generate smaller git diffs. Our install script installs a package that automatically runs these formatters when you attempt to push. If there are any changes to format, it puts those changes in git's unstaged changes. If this happens, commit the format changes and push again.

Linting:

We use mypy to check python typings. Run:

mypy .

We also use import-linter to enforce package dependency rules. The rules are defined in a config file here. To run the linter:

lint-imports

Investigating slow pages

We have a built in tool to help us:

We can collect an execution profile and visualize as a flamegraph. This requires a few more steps but is much more comprehensive. See below for the detailed steps.

Generating flamegraphs of profiling information:

We have a hook for generating flame graphs for any request as a quick and dirty way to get profiling information from either prod or a development environment.

This is now controlled by a cookie which you can configure by going to /profiler/config (e.g. http://127.0.0.1:5000/profiler/config or https://cds.team/depmap/profiler/config )

The more profiling enabled, the slower requests will be because profiling adds overhead so best results will be to target what you want profiled. A good starting point is listing the following in "Modules to trace":

werkzeug.*
flask.*
depmap.*

(Timings are collected for all calls that are made from a function in modules that match the regular expressions in "Modules to trace". Once a call is made outside one of those modules, tracing is disabled until the function returns.)

To see collected profiles go to /profiler/profiles and the newest profiles will be at the top. Click "View" to open the profile.

Error Reporting

We use stackdriver for error reporting, and have it automatically create a pivotal task when it encounters an error.

Back end python errors are automatically reported to stackdriver.

Front end errors must be manually reported (there is a pivotal task to auto report). The global javascript variable errorHandler can be used to report manually errors to stackdriver. Use errorHandler.report(\'\<information about error\>\') to report errors.

This errorHandler is mocked out in dev, to cause an alert instead of sending to stackdriver. If stackdriver integration needs testing in dev, temporariliy modify the test for the dev environment in layout.html for loading and initializing the errorHandler.

Database Build Overview

The database build step takes the outputs of the preprocessing pipeline in the s3 bucket and loads them into the database. To build the database locally, run ./flask recreate_full_db. To build the database remotely and store it for download during deployment, see the db build steps in Jenkins http://datasci-dev.broadinstitute.org:8080/view/depmap/.

To build the db locally, run:

./flask recreate_dev_db

Deployment Overview

To deploy the latest successful build from travis, run the appropriate jenkins job here http://datasci-dev.broadinstitute.org:8080/view/depmap/job/DepMap%20Staging%20Environments/

Scripts for jenkins jobs are found in the depmap-deploy repo at https://github.com/broadinstitute/depmap-deploy

The final docker run command with -v directory mounts is found in the depmap-flask script in the ansible-configs repo which

Invalidating and re-loading a nonstandard dataset

We specify nonstandard, interactive-only datasets in internal.py (e.g. for the internal environment), in the internal_nonstandard_datasets dictionary. This dictionary is handwritten and hand-curated, according to various people's requests to add datasets.

Sometimes, we make a mistake with this curation, e.g. by setting the wrong transpose or failing to set use_arxspan_id. If these mistakes are used to load the database, the database gets loaded with nonstandard matrix indices of the wrong configuration.

This mistakes often happen, and so we want to have a way to invalidate and re-load these datasets without having to load the entire database. Thus, the load steps in db_load_commands have two parts in separate transactions. 1) loop through all nonstandard datasets and run delete_cache_if_invalid_exists. 2) loop through all nonstandard datasets and add if they do not exist.

delete_cache_if_invalid_exists checks the validity of a cache by checking if the transpose value of what is currently loaded matches the transpose value in the current config. This decision to only store and check the transpose is somewhat arbitrary, and could definitely be extended to store and check other options that affect db load, if the use case arises.

If a dataset was loaded with the wrong transpose option, simply change it to the correct one and rebuild the db (reploying staging might also just work).

If a dataset was loaded incorrectly another way (e.g. not using arxspan ids), one can invalidate the cache by changing the value of transpose. Push the branch with this changed transpose, and let the travis job build. Then, run the build db jenkins job with the 'USE_PREVIOUS' option. This should run delete_cache_if_invalid_exists, then complete the transaction. The next loop/transaction (loading the dataset) will typically fail due to the incorrect transpose; this is fine. After the job completes, the first loop/transaction that deleted the cache should be persisted and stored. So now change transpose to the correct value, push the branch, then let the db build again with the 'USE_PREVIOUS' option. The second loop/transaction should now run and load the dataset correctly.

The db load does not delete datasets that may have been previously loaded and are in the db, but are no longer in the config.

Access Controls

The access control layer (primarily implemented in depmap.access_control) hides rows depending on the current user as reported in a header field on the request. (This header is added to the request when it passes through oauth2_proxy.)

Authentication

For deployments with HAS_ACCESS_CONTROL=True, we expect requests to be authenticated and signed by oauth. This is enforced by doing a signature check registered in flask's before_request.

For token authentication, oauth supports basic authentication derived from the usernames and passwords in the oauth2-htpassd file for the respective server. To generate a token for a user: :

import base64
token = base64.b64encode("<insert username>:<insert password>".encode('ascii'))

Testing with private data in the webapp

In order to see what a user can see, all "admin" users (specified in the access control config) have the ability to switch what username is used for purposes of filtering the database. Going to http://localhost:5000/access_control/override will allow admins to pretend to be a different user and will reflect what that user can see.

Making queries with access controls in flask shell

A request context is needed to provide an owner_id, which is needed for queries on tables with access controls. Attempts to query these tables without a request context will generate the following error. :

OperationalError: (sqlite3.OperationalError) user-defined function raised exception

We have set up the flask shell command to automatically creates a request context. However, this is not present if running something outside of context, e.g. when using the python library timeit. To create a request context, include [from flask import current_app; current_app.test_request_context().push()]{.title-ref} in the timeit setup.

Making queries with access controls in sqlite3

Given a python sqlalchemy query, the raw sql statement can be obtained by str(query). However, if this query involves tables with access controls, directly executing it in the sqlite3 command line tool will give the following error.:

Error: no such function: owned_by_is_visible

To get around this error, names of tables must be changed to their write_only versions. E.g., :

select * from dataset; # instead of this
select * from dataset_write_only; # should be this

Instructions for adding a new dataset

There are some steps that might be expected for adding a new dataset, e.g.

1. adding a DependencyDataset/BiomarkerDataset enum or a new model (e.g. Mutation), with display name and units specified in shared.py
2. adding any necessary pipeline steps
3. adding a db load step. it should use log_data_issue for data issues (e.g. gene not found)
4. generating sample data with appropriate holes

Other requirements that might not be obvious are:

1. Every dataset in the portal should have a corresponding download entry. Add a download entry for this new dataset in \_all_internal.py or \_all_public.py depending on whether it is public. The downloads list appears in the order they are specified, so put the dataset in an appropriate position (i.e. probably not before the quarterly depmap releases). If the dataset is public and not already hosted externally, upload the dataset to taiga (if it is not already there), download it, then re-upload it to the public download bucket (see section "Uploading to public/dmc download bucket").
2. Add to settings in internal.py/external.py. Examples of variable names are given for internal.

• Add the dataset enum to the list of datasets (internal_datasets). If associations are computed, also add it to association_deps or association_bioms.
• If the dataset has a version that should be appended to its display name, add it to the dataset versions (internal_versions). All datasets that are regenerated multiple times (e.g., quarterly) need a version.

3. Check if the dataset applies to an is_ selectors on the DependencyDataset model. E.g. is_rnai, is_compound_related.
4. Does this dataset involve cell lines? Most likely yes. If so, add it to the enums list/table of cell line memberships in cell_line/views.py.
5. Add to announcements/changelog
6. Should the dataset be added to headliners? If so, add to headliners in internal_download_settings and generate the SummaryStats.
7. Is this dataset an "important" one, that should be prioritized in dropdown lists? If so, add a global_priority to its dataset instance.

Pipeline and db load steps for this new dataset can be tried out on real data through a custom branch deployment: https://docs.google.com/document/d/1SsEUGJzROxw37_-NdU3jLl_v7czwCqiry1cgaVLdD9c/edit#heading=h.v6k5gz8t7nsm

Uploading to public/dmc download bucket

Please know that these instructions are stale, the CLI command has changed. Please see the code for download_taiga_and_upload

For routine quartely releases, see the release task in https://app.asana.com/0/1156387482589290/1156388333407152/f

Sometimes, we use data from third parties, and provide them for direct download without any transformation. For these, we just put them on taiga and re-upload them to a bucket. The public bucket (accessible from all environments) is depmap-external-downloads, under the Achilles project https://console.cloud.google.com/storage/browser/depmap-external-downloads. The DMC-only bucket is at https://console.cloud.google.com/storage/browser/depmap-dmc-downloads. The bucket structure should contain the taiga id.

Sometimes, we transform data in the portal (e.g. unify cell line/gene/compound names), and make these modified versions available for download. For these, we first put the data in taiga under processed portal downloads https://cds.team/taiga/folder/ec5dfb868a46467daa17f03ee61b3afa. The file name uploaded to taiga should be the file name we want when people download the file. To describe how the data was transformed, so please include the requested provenance in the taiga dataset description. The portal changes over time, so this provenance is important. Now that this dataset has a taiga id, the bucket path should include this taiga id (see code below).

After the data is on Taiga, we have a flask cli command download_taiga_and_upload that facilities easy upload. Fill in the desired BucketUrl for the DownloadFile(s) you would like to upload. This BucketUrl should be structured <subfolder>/<taiga name>.<version>/<taiga file name>, e.g. processed_portal_downloads/depmap-public-cell-line-metadata-183e.1/DepMap-2018q4-celllines.csv for a processed portal download (export from db), or drug/primary-screen-e5c7.1/primary_merged_row_meta.csv for a direct taiga re-upload.

Then, in the upload_download_commands.py file, fill in the files_to_upload dictionary with the release name, file names, and taiga formats for the files to be uploaded. Modify the flask script to use the appropriate environment for public/dmc (xstaging or dstaging). Then run :

./flask download_taiga_and_upload <env>
# where <env> is xstaging or dstaging

The env parameter helps us make sure we don't accidently upload e.g. an internal file into the public bucket, since the env limits the downloads available.

Retracting a download file

See the DepMap Portal Operations google doc https://docs.google.com/document/d/1M9K6WkJQo5_9DDXnJWTUZQhE37wxZDCpIIfVZmM_Blg/edit#heading=h.fr8mxpr1nvjc

Creating a new React page

This will step you through the process of creating a new Flask route and mapping it to an interactive page that can be developed as a React component. Refer to this guide when you're adding new functionality to the Portal that makes sense as its own standalone page.

First a bit of Portal frontend history

The Portal began life as a Flask app that leveraged Jinja templates to render all of its HTML. jQuery was used to sprinkle in some limited interactivity. A few such “old school” pages (notably the landing page) still exist.

After some time, we transitioned to using React as a frontend framework. This would lend itself to more interactive experiences and make it easier to develop and maintain the frontend code.

Initially this took the form of a global DepMap JavaScript object that had methods like DepMap.initDownloadsPage() and DepMap.initCellLinePage() that could be called to initialize React on the page. This was not very efficient because it meant all the code for every page was being delivered to the browser as one massive file.

By that time we were already using Webpack as a means to deliver 3rd party libraries alongside our application code. Webpack puts them together into one JS file known as a “bundle.” We then modified the Webpack configuration to output separate bundles for each page. Those DepMap.initXYZPage() methods went away. Instead each HTML page would have a <script> tag that loads a dedicated JS file built specifically to work with it and that automatically bootstraps itself as a React app.

Note that the global DepMap object still exists today. Its usage is now much more limited. It acts as a convenient place for methods like DepMap.launchContextManagerModal() that launches a modal window from the navbar. It's an example of some complicated React code that doesn't map directly to a specific page.

Ultimately we settled on a solution that still uses Flask for routing. Each page still has its own Jinja template. The difference is that the template is very basic. It does just enough to load our navbar and load the correct React bundle for that page.

Step-by-step guide

Hopefully you now have a feel for how things are structured and why. Creating a new page will consist of the following steps:

• Create a Jinja template
• Set up the routing in Flask
• Create a new React app
• Configure Webpack

In the examples below, the name MY_APP will act as a placeholder for the name of your page.

Step #1: Create a Jinja template

In depmap/portal-backend/depmap/templates/MY_APP/ create a new index.html file. Its contents should look like this.

{% extends "full_page.html" %}

{% block page_title %}
    {# The title that will appear in the browser's title/tab bar #}
{% endblock %}

{% block meta_description %}
    {# include a short description that search engines can display #}
{% endblock %}

{% block content %}
    <div class='full-screen-div'>
        {% include "nav_footer/nav.html" %}
        {# Replace MY_APP with the name of your page #}
        <div id="MY_APP"></div>
    </div>
{% endblock %}

{% block js %}
    {# Replace MY_APP with the name of your page. Note the -data suffix. #}
    <script id="MY_APP-data" type="application/json">
      {
          {# Any data that needs to be present
          when your app starts up can go here. #}
          "secretOfTheUniverse": 42
      }
    </script>
    {# Replace MY_APP with the name of your page #}
    <script src="{{ webpack_url('MY_APP.js') }}"></script>
{% endblock %}

Step #2: Set up the routing in Flask

In depmap/portal-backend/depmap/MY_APP/ create a new views.py file. Its contents should look like this.

from flask import Blueprint, render_template

blueprint = Blueprint(
    "MY_APP",
    __name__,
    url_prefix="/MY_APP",
    static_folder="../static",
)


@blueprint.route("/")
def view_MY_APP():
    """
    Entry point
    """
    return render_template("MY_APP/index.html")

👉 Make sure to import it here and register it here.

Step #3: Create a new React app

In depmap/frontend/packages/portal-frontend/src/apps/ create a new MY_APP.tsx file. Its contents should look like this.

import "src/public-path";
import React from "react";
import ReactDOM from "react-dom";
import ErrorBoundary from "src/common/components/ErrorBoundary";

const container = document.getElementById("MY_APP");
const dataElement = document.getElementById("MY_APP-data");
if (!dataElement || !dataElement.textContent) {
  throw new Error(
    `Expected a DOM element like <script type="application/json">{ ... }</script>'`
  );
}

const data = JSON.parse(dataElement.textContent);
const { secretOfTheUniverse } = data;

const App = () => {
  return (
    <ErrorBoundary>
      <div>
        The answer to life, the universe, and everything is:
        {secretOfTheUniverse}
      </div>
    </ErrorBoundary>
  );
};

ReactDOM.render(<App />, container);

Step #4: Configure Webpack

Now Webpack needs to know that your app should be considered its own bundle. To the webpack config, add this line:

    "MY_APP": "./src/apps/MY_APP.tsx",

Note: You'll have to restart Webpack Dev Server for this change to be recognized.

If everything worked correctly you should be able to navigate to http://127.0.0.1:5000/MY_APP/ and see your new page!