Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/arxiv/arxiv-browse

Flask app for article abstract and listing pages
https://github.com/arxiv/arxiv-browse

arxiv-ce flask in-production python

Last synced: 10 days ago
JSON representation

Flask app for article abstract and listing pages

Awesome Lists containing this project

README 

        
# arxiv-browse



## Running Browse with the Flask development server



You can run the browse app directly.



```bash

make venv

````



(the make rarely works)



or 



```bash

python --version

# 3.11.x

python -m venv ./venv

source ./venv/bin/activate

pip install poetry==1.3.2

poetry install

python main.py

```

Note -- make sure you have python dev installed befoore doing the above steps, or the `poetry install` will fail trying to build the mySQL library dependency. E.g.: `sudo apt-get install python3.11-dev`



Then go to http://127.0.0.1:8080/abs/0906.5132



This will monitor for any changes to the Python code and restart the server.

Unfortunately static files and templates are not monitored, so you'll have to

manually restart to see those changes take effect.



By default, the application will use the directory trees in

`tests/data/abs_files` and `tests/data/cache` and when looking for the document

metadata and PDF files. These paths can be overridden via environment variables

(see `browse/config.py`).



This method will only give you access to minimal data in the built-in test

dataset. For full (read-only) access to the production database, the following

steps are necessary:



## Running with access to the production database



Prerequisites:

you are logged into gcloud and have default application credentials. This

can be achieved by calling `gcloud auth login --update-adc --force` and

logging into your @arxiv.org account.



Next, **all** the following steps have to be done.



Also, in the following we assume that you two port variable set in the environment:

```

MAIN_DB_PORT=3301

LATEXML_DB_PORT=3302

```

(the numbers are not important, but must be different)



### Create a .env file



First, you'd need to create the '.env' file somewhere. Using tests/.env is suggested.



```

DOCUMENT_ABSTRACT_SERVICE=browse.services.documents.db_docs

ABS_PATH_ROOT=gs://arxiv-production-data

DOCUMENT_CACHE_PATH=gs://arxiv-production-data/ps_cache

DOCUMENT_LISTING_PATH=gs://arxiv-production-data/ftp

DISSEMINATION_STORAGE_PREFIX=gs://arxiv-production-data

LATEXML_ENABLED=True

LATEXML_BUCKET="gs://latexml_document_conversions"

LATEXML_BASE_URL=//127.0.0.1:8080

FLASKS3_ACTIVE=1

CLASSIC_DB_URI=" SEE BELOW "

LATEXML_DB_URI=" SEE BELOW "

```



The value of `CLASSIC_DB_URI` one can obtain by

```

MAIN_SECRET=$(gcloud secrets versions access latest --project=arxiv-production  --secret=readonly-arxiv-db-uri)

echo $MAIN_SECRET | sed -e "s#/arXiv.*#127.0.0.1:${MAIN_DB_PORT}/arXiv#"

```



The value of `LATEXML_DB_URI` one can obtain by

```

LATEXML_SECRET=$(gcloud secrets versions access latest --project=arxiv-production  --secret=latexml_db_uri_psycopg2)

echo $LATEXML_SECRET | sed -e "s#/latexmldb.*#127.0.0.1:${LATEXML_DB_PORT}/latexmldb#"

```



If you have a PyCharm,

script: main.py

Enable env files

   Add tests/.env



![docs/development/pycharm-run-setting.png](docs/development/pycharm-run-setting.png)



### Running cloud-sql-proxy



You can obtain the database name `MAIN_DB_NAME` from the same `$SECRET` as in the previous step:

```

MAIN_DB_NAME=$(echo $MAIN_SECRET | sed -e "s#^.*unix_socket=/cloudsql/##")

```



Similar, for the `LATEXML_DB_NAME` one needs to do

```

LATEXML_DB_NAME=$(echo $LATEXML_SECRET | sed -e "s#^.*host=/cloudsql/##")

```



NOTE: `cloud_sql_proxy` and `cloud-sql-proxy` (new) have different options.



```

cloud-sql-proxy --address 0.0.0.0 --port ${MAIN_DB_PORT} ${MAIN_DB_NAME}

cloud-sql-proxy --address 0.0.0.0 --port ${LATEXML_DB_PORT} ${LATEXML_DB_NAME}

```



For the old version

```

cloud_sql_proxy --instances=${MAIN_DB_NAME}=tcp:${MAIN_DB_PORT}

cloud_sql_proxy --instances=${LATEXML_DB_NAME}=tcp:${LATEXML_DB_PORT}

```



If the proxy is working, you can use mysql client to connect to the db.



```bash

mysql -u browse -p --host 127.0.0.1 --port ${MAIN_DB_PORT} arXiv

Enter password: 

...

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.



mysql> show tables;

+------------------------------------------+

| Tables_in_arXiv                          |

+------------------------------------------+

| Subscription_UniversalInstitution        |

````



### Run the main server



Run

```

python main.py`

```

should start up and run 



### Test suite



Run the main test suite with the following command:



```bash

pytest tests

```



### Running Browse in Docker

You can also run the browse app in Docker. The following commands will build and

run browse using defaults for the configuration parameters and will use the test

data from `tests/data`. Install [Docker](https://docs.docker.com/get-docker/) if

you haven't already, then run the following:



```bash

script/start

```



This command will build the docker image and run it. If all goes well,

http://localhost:8000/ will render the home page.



### Configuration Parameters



See `browse/config.py` for configuration parameters and defaults). Any of these

can be overridden with environment variables.



### Serving static files on S3



We use [Flask-S3](https://flask-s3.readthedocs.io/en/latest/) to serve static

files via S3.



After looking up the AWS keys and region and bucket:

```bash

cd arxiv-browse

git pull

AWS_ACCESS_KEY_ID=x AWS_SECRET_ACCESS_KEY=x \

 AWS_REGION=us-east-1 FLASKS3_BUCKET_NAME=arxiv-web-static1 \

 pipenv run python upload_static_assets.py

```



In AWS -> CloudFront, select the static.arxiv.org distribution, -> Invalidations -> Create invalidation,

and enter a list of url file paths, eg: /static/browse/0.3.4/css/arXiv.css.



It may be help to use a web browser's inspect->network to find the active release version.



### Tests and linting for PRs

There is a github action that runs on PRs that merge to develop. PRs for which

these tests fail will be blocked. It is the equivalent of running:



```

# if there are Python syntax errors or undefined names

flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics



pytest tests

```



### Setting up pytest in PyCharm



![docs/development/pycharm-run-setting.png](docs/development/pycharm-pytest.png)