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README for isamples_inabox

Note: This work is in active development and likely to change considerably, including split / merge to other repositories.

Provides implementation of scripts for harvesting content from repositories, placing the content in a postgres database, relations in a Solr index, a Fast-API implementation for accessing the content and a simple UI for viewing.

Installation

Python environment

Follow the instructions in python_setup.md.html

Python tooling

Before code is allowed to merge, it needs to pass flake8 and mypy checks. You may follow the instructions on how to install and run these locally. Additionally, you may run the black python formatter on new code to ensure the formatting matches the rest of the project.

Tunneling postgres and solr configuration

If you don't want to worry about running everything locally, you can tunnel remote services with ssh. For example, with these two ssh tunnels:

solr

ssh <username>@mars.cyverse.org -p 1657 -L8984:localhost:9983

postgres

ssh <username>@mars.cyverse.org -p 1657 -L6432:localhost:5432

we would end up with iSB config that looks like

db_url = "postgresql+psycopg2://isb_writer:<password>@localhost:6432/isb_1"
solr_url = "http://localhost:8984/solr/isb_core_records/"

Note that you'll want that config file to be named isb_web_config.env and located in the working directory of where you run whatever script you're working on. After that, run the script with

poetry run python example_script.py --config isb_web_config.env

Local postgres and solr configuration

If you'd prefer to run everything locally, follow this.

Install Postgres and Solr, e.g.:

brew install postgres
brew install solr

Edit solr configuration to start in cloud mode:

edit /usr/local/Cellar/solr/8.8.2/homebrew.mxcl.solr.plist and add:

<string>-c</string>

under <key>ProgramArguments</key>

Start Solr and postgres:

brew services start postgres
brew services start solr

Running the iSamples Central Postgres db locally

Given that the iSamples Central database is pretty large, you'll want to start with a dump of the existing iSamples Central database rather than attempting to recreate it by hand. Note that these steps do take quite some time to run, so don't be alarmed if it seems like nothing is happening.

The first thing you'll want to do is dump the postgres database (or grab it from /var/local/data/ on mars.cyverse.org). The following command will dump an existing iSC postgres database and create a .sql file that you will load up in your local database:

pg_dump -a -U isb_writer -h localhost -d isb_1 > isamples_data_only.sql -- note that the -a switch specifies data-only. Given the history of the project and the rate at which things change, it is safer to not include the table creation statements in the dumped .sql file.

Then, you'll want to transfer that dumped file to your local machine. It's likely faster to gzip it first on the server and gunzip it locally. Once you've transferred to your local machine, bringing up a local Docker iSB container will create the necessary tables and indexes so that the load may proceed. After you've done that (and created the necessary tables and indexes), you may load up the postgres dump like so:

psql -d isb_1 -f isamples_data_only.sql

Python virtual environment creation

Create a python virtual environment, checkout the source, and run poetry install.

e.g.:

mkvirtualenv isb-dev
git clone [email protected]:isamplesorg/isamples_inabox.git
cd isamples_inabox
git checkout -b origin/develop
poetry install

If running locally, create a database, e.g:

psql postgres
CREATE DATABASE isb_1;
CREATE USER isb_writer WITH ENCRYPTED PASSWORD 'some_password';
GRANT ALL PRIVILEGES ON DATABASE isb_1 TO isb_writer;

Create a config file, e.g.:

# cat isb.cfg
db_url = "postgresql+psycopg2://isb_writer:some_password@localhost/isb_1"
max_records = 1000
verbosity="INFO"

If running locally, create a solr collection isb_core_records:

solr create -c isb_core_records

Then run the schema creation script against your local solr instance:

python scripts/solr_schema_init/create_isb_core_schema.py

Operation

Populate the database with 5000 SESAR records:

workon isb-dev  #activate virtual environment if necessary
sesar_things --config isb.cfg load -m 5000

Populate the solr index with relations in those SESAR records:

sesar_things --config isb.cfg relations

Web service

Run the fastAPI server in dev mode like:

workon isb-dev  #activate virtual environment if necessary
python isb_web/main.py

Navigate to http://localhost:8000/